Alternative splicing. Medical search

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.

Complement activation initiated by the interaction of microbial ANTIGENS with COMPLEMENT C3B. When COMPLEMENT FACTOR B binds to the membrane-bound C3b, COMPLEMENT FACTOR D cleaves it to form alternative C3 CONVERTASE (C3BBB) which, stabilized by COMPLEMENT FACTOR P, is able to cleave multiple COMPLEMENT C3 to form alternative C5 CONVERTASE (C3BBB3B) leading to cleavage of COMPLEMENT C5 and the assembly of COMPLEMENT MEMBRANE ATTACK COMPLEX.

Procedures, such as TISSUE CULTURE TECHNIQUES; mathematical models; etc., when used or advocated for use in place of the use of animals in research or diagnostic laboratories.

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.

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.

Therapeutic practices which are not currently considered an integral part of conventional allopathic medical practice. They may lack biomedical explanations but as they become better researched some (PHYSICAL THERAPY MODALITIES; DIET; ACUPUNCTURE) become widely accepted whereas others (humors, radium therapy) quietly fade away, yet are important historical footnotes. Therapies are termed as Complementary when used in addition to conventional treatments and as Alternative when used instead of conventional treatment.

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

Different forms of a protein that may be produced from different GENES, or from the same gene by ALTERNATIVE SPLICING.

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.

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.

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

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

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.

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

A glycine-rich, heat-labile serum glycoprotein that contains a component of the C3 CONVERTASE ALTERNATE PATHWAY (C3bBb). Bb, a serine protease, is generated when factor B is cleaved by COMPLEMENT FACTOR D into Ba and Bb.

Evaluation undertaken to assess the results or consequences of management and procedures used in combating disease in order to determine the efficacy, effectiveness, safety, and practicability of these interventions in individual cases or series.

The sequential activation of serum COMPLEMENT PROTEINS to create the COMPLEMENT MEMBRANE ATTACK COMPLEX. Factors initiating complement activation include ANTIGEN-ANTIBODY COMPLEXES, microbial ANTIGENS, or cell surface POLYSACCHARIDES.

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

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

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.

Elements of limited time intervals, contributing to particular results or situations.

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

Established cell cultures that have the potential to propagate indefinitely.

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.

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 glycoprotein that is central in both the classical and the alternative pathway of COMPLEMENT ACTIVATION. C3 can be cleaved into COMPLEMENT C3A and COMPLEMENT C3B, spontaneously at low level or by C3 CONVERTASE at high level. The smaller fragment C3a is an ANAPHYLATOXIN and mediator of local inflammatory process. The larger fragment C3b binds with C3 convertase to form C5 convertase.

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 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.

Theoretical representations that simulate the behavior or activity of biological processes or diseases. For disease models in living animals, DISEASE MODELS, ANIMAL is available. Biological models include the use of mathematical equations, computers, and other electronic equipment.

The statistical reproducibility of measurements (often in a clinical context), including the testing of instrumentation or techniques to obtain reproducible results. The concept includes reproducibility of physiological measurements, which may be used to develop rules to assess probability or prognosis, or response to a stimulus; reproducibility of occurrence of a condition; and reproducibility of experimental results.

The addition of a tail of polyadenylic acid (POLY A) to the 3' end of mRNA (RNA, MESSENGER). Polyadenylation involves recognizing the processing site signal, (AAUAAA), and cleaving of the mRNA to create a 3' OH terminal end to which poly A polymerase (POLYNUCLEOTIDE ADENYLYLTRANSFERASE) adds 60-200 adenylate residues. The 3' end processing of some messenger RNAs, such as histone mRNA, is carried out by a different process that does not include the addition of poly A as described here.

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

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.

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.

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

Binary classification measures to assess test results. Sensitivity or recall rate is the proportion of true positives. Specificity is the probability of correctly determining the absence of a condition. (From Last, Dictionary of Epidemiology, 2d ed)

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

A serine protease that is the complex of COMPLEMENT C3B and COMPLEMENT FACTOR BB. It cleaves multiple COMPLEMENT C3 into COMPLEMENT C3A (anaphylatoxin) and COMPLEMENT C3B in the ALTERNATIVE COMPLEMENT ACTIVATION PATHWAY.

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.

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).

Complement activation initiated by the binding of COMPLEMENT C1 to ANTIGEN-ANTIBODY COMPLEXES at the COMPLEMENT C1Q subunit. This leads to the sequential activation of COMPLEMENT C1R and COMPLEMENT C1S subunits. Activated C1s cleaves COMPLEMENT C4 and COMPLEMENT C2 forming the membrane-bound classical C3 CONVERTASE (C4B2A) and the subsequent C5 CONVERTASE (C4B2A3B) leading to cleavage of COMPLEMENT C5 and the assembly of COMPLEMENT MEMBRANE ATTACK COMPLEX.

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

The 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)

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

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

A 53-kDa protein that is a positive regulator of the alternate pathway of complement activation (COMPLEMENT ACTIVATION PATHWAY, ALTERNATIVE). It stabilizes the ALTERNATIVE PATHWAY C3 CONVERTASE (C3bBb) and protects it from rapid inactivation, thus facilitating the cascade of COMPLEMENT ACTIVATION and the formation of MEMBRANE ATTACK COMPLEX. Individuals with mutation in the PFC gene exhibit properdin deficiency and have a high susceptibility to infections.

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

The different gene transcripts generated from a single gene by RNA EDITING or ALTERNATIVE SPLICING of RNA PRECURSORS.

A serum protein which is important in the ALTERNATIVE COMPLEMENT ACTIVATION PATHWAY. This enzyme cleaves the COMPLEMENT C3B-bound COMPLEMENT FACTOR B to form C3bBb which is ALTERNATIVE PATHWAY C3 CONVERTASE.

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

The determination of the pattern of genes expressed at the level of GENETIC TRANSCRIPTION, under specific circumstances or in a specific cell.

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.

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

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

The 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.

Serine proteases that cleave COMPLEMENT C3 into COMPLEMENT C3A and COMPLEMENT C3B, or cleave COMPLEMENT C5 into COMPLEMENT C5A and COMPLEMENT C5B. These include the different forms of C3/C5 convertases in the classical and the alternative pathways of COMPLEMENT ACTIVATION. Both cleavages take place at the C-terminal of an ARGININE residue.

Computer-based representation of physical systems and phenomena such as chemical processes.

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

The 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.

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.

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

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

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

The act of making a selection among two or more alternatives, usually after a period of deliberation.

Genotypic differences observed among individuals in a population.

Proteins prepared by recombinant DNA technology.

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

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

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

The rate dynamics in chemical or physical systems.

Statistical formulations or analyses which, when applied to data and found to fit the data, are then used to verify the assumptions and parameters used in the analysis. Examples of statistical models are the linear model, binomial model, polynomial model, two-parameter model, etc.

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

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

The larger fragment generated from the cleavage of COMPLEMENT C3 by C3 CONVERTASE. It is a constituent of the ALTERNATIVE PATHWAY C3 CONVERTASE (C3bBb), and COMPLEMENT C5 CONVERTASES in both the classical (C4b2a3b) and the alternative (C3bBb3b) pathway. C3b participates in IMMUNE ADHERENCE REACTION and enhances PHAGOCYTOSIS. It can be inactivated (iC3b) or cleaved by various proteases to yield fragments such as COMPLEMENT C3C; COMPLEMENT C3D; C3e; C3f; and C3g.

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.

Proteins found in any species of bacterium.

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 method of comparing the cost of a program with its expected benefits in dollars (or other currency). The benefit-to-cost ratio is a measure of total return expected per unit of money spent. This analysis generally excludes consideration of factors that are not measured ultimately in economic terms. Cost effectiveness compares alternative ways to achieve a specific set of results.

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.

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.

A cell line derived from cultured tumor cells.

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 multistage process that includes cloning, physical mapping, subcloning, sequencing, and information analysis of an RNA SEQUENCE.

The part of CENTRAL NERVOUS SYSTEM that is contained within the skull (CRANIUM). Arising from the NEURAL TUBE, the embryonic brain is comprised of three major parts including PROSENCEPHALON (the forebrain); MESENCEPHALON (the midbrain); and RHOMBENCEPHALON (the hindbrain). The developed brain consists of CEREBRUM; CEREBELLUM; and other structures in the BRAIN STEM.

A family of ribonucleoproteins that were originally found as proteins bound to nascent RNA transcripts in the form of ribonucleoprotein particles. Although considered ribonucleoproteins they are primarily classified by their protein component. They are involved in a variety of processes such as packaging of RNA and RNA TRANSPORT within the nucleus. A subset of heterogeneous-nuclear ribonucleoproteins are involved in additional functions such as nucleocytoplasmic transport (ACTIVE TRANSPORT, CELL NUCLEUS) of RNA and mRNA stability in the CYTOPLASM.

Studies in which individuals or populations are followed to assess the outcome of exposures, procedures, or effects of a characteristic, e.g., occurrence of disease.

An important soluble regulator of the alternative pathway of complement activation (COMPLEMENT ACTIVATION PATHWAY, ALTERNATIVE). It is a 139-kDa glycoprotein expressed by the liver and secreted into the blood. It binds to COMPLEMENT C3B and makes iC3b (inactivated complement 3b) susceptible to cleavage by COMPLEMENT FACTOR I. Complement factor H also inhibits the association of C3b with COMPLEMENT FACTOR B to form the C3bB proenzyme, and promotes the dissociation of Bb from the C3bBb complex (COMPLEMENT C3 CONVERTASE, ALTERNATIVE PATHWAY).

Proteins found in plants (flowers, herbs, shrubs, trees, etc.). The concept does not include proteins found in vegetables for which VEGETABLE PROTEINS is available.

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

Use of plants or herbs to treat diseases or to alleviate pain.

Studies used to test etiologic hypotheses in which inferences about an exposure to putative causal factors are derived from data relating to characteristics of persons under study or to events or experiences in their past. The essential feature is that some of the persons under study have the disease or outcome of interest and their characteristics are compared with those of unaffected persons.

Proteins encoded by the mitochondrial genome or proteins encoded by the nuclear genome that are imported to and resident in the MITOCHONDRIA.

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

Hybridization of a nucleic acid sample to a very large set of OLIGONUCLEOTIDE PROBES, which have been attached individually in columns and rows to a solid support, to determine a BASE SEQUENCE, or to detect variations in a gene sequence, GENE EXPRESSION, or for GENE MAPPING.

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.

Sequences within RNA that regulate the processing, stability (RNA STABILITY) or translation (TRANSLATION, GENETIC) of RNA.

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.

Serum glycoproteins participating in the host defense mechanism of COMPLEMENT ACTIVATION that creates the COMPLEMENT MEMBRANE ATTACK COMPLEX. Included are glycoproteins in the various pathways of complement activation (CLASSICAL COMPLEMENT PATHWAY; ALTERNATIVE COMPLEMENT PATHWAY; and LECTIN COMPLEMENT PATHWAY).

A RNA-binding protein that binds to polypyriminidine rich regions in the INTRONS of messenger RNAs. Polypyrimidine tract-binding protein may be involved in regulating the ALTERNATIVE SPLICING of mRNAs since its presence on an intronic RNA region that is upstream of an EXON inhibits the splicing of the exon into the final mRNA product.

Endogenous proteins that inhibit or inactivate COMPLEMENT C3B. They include COMPLEMENT FACTOR H and COMPLEMENT FACTOR I (C3b/C4b inactivator). They cleave or promote the cleavage of C3b into inactive fragments, and thus are important in the down-regulation of COMPLEMENT ACTIVATION and its cytolytic sequence.

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

Observation of a population for a sufficient number of persons over a sufficient number of years to generate incidence or mortality rates subsequent to the selection of the study group.

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

Proteins 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.

New abnormal growth of tissue. Malignant neoplasms show a greater degree of anaplasia and have the properties of invasion and metastasis, compared to benign neoplasms.

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.

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.

The process of cumulative change over successive generations through which organisms acquire their distinguishing morphological and physiological characteristics.

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

Alternatives to the use of animals in research, testing, and education. The alternatives may include reduction in the number of animals used, replacement of animals with a non-animal model or with animals of a species lower phylogenetically, or refinement of methods to minimize pain and distress of animals used.

Structurally related forms of an enzyme. Each isoenzyme has the same mechanism and classification, but differs in its chemical, physical, or immunological characteristics.

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

A 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).

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

A class of closely related heterogeneous-nuclear ribonucleoproteins of approximately 34-40 kDa in size. Although they are generally found in the nucleoplasm, they also shuttle between the nucleus and the cytoplasm. Members of this class have been found to have a role in mRNA transport, telomere biogenesis and RNA SPLICING.

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

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

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.

The sequence at the 3' end of messenger RNA that does not code for product. This region contains transcription and translation regulating sequences.

The systematic study of the complete DNA sequences (GENOME) of organisms.

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

Application of statistical procedures to analyze specific observed or assumed facts from a particular study.

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

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

Any of the processes by which nuclear, cytoplasmic, or intercellular factors influence the differential control of gene action during the developmental stages of an organism.

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.

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

Progressive restriction of the developmental potential and increasing specialization of function that leads to the formation of specialized cells, tissues, and organs.

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.

Naturally occurring or experimentally induced animal diseases with pathological processes sufficiently similar to those of human diseases. They are used as study models for human diseases.

Substances that reduce the growth or reproduction of BACTERIA.

The relationship between the dose of an administered drug and the response of the organism to the drug.

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

Post-transcriptional biological modification of messenger, transfer, or ribosomal RNAs or their precursors. It includes cleavage, methylation, thiolation, isopentenylation, pseudouridine formation, conformational changes, and association with ribosomal protein.

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

Methods of creating machines and devices.

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 genetic complement of an organism, including all of its GENES, as represented in its DNA, or in some cases, its RNA.

Proteins that originate from insect species belonging to the genus DROSOPHILA. The proteins from the most intensely studied species of Drosophila, DROSOPHILA MELANOGASTER, are the subject of much interest in the area of MORPHOGENESIS and development.

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 complete genetic complement contained in the DNA of a set of CHROMOSOMES in a HUMAN. The length of the human genome is about 3 billion base pairs.

Organelles in which the splicing and excision reactions that remove introns from precursor messenger RNA molecules occur. One component of a spliceosome is five small nuclear RNA molecules (U1, U2, U4, U5, U6) that, working in conjunction with proteins, help to fold pieces of RNA into the right shapes and later splice them into the message.

Studies determining the effectiveness or value of processes, personnel, and equipment, or the material on conducting such studies. For drugs and devices, CLINICAL TRIALS AS TOPIC; DRUG EVALUATION; and DRUG EVALUATION, PRECLINICAL are available.

Studies to determine the advantages or disadvantages, practicability, or capability of accomplishing a projected plan, study, or project.

Family in the order COLUMBIFORMES, comprised of pigeons or doves. They are BIRDS with short legs, stout bodies, small heads, and slender bills. Some sources call the smaller species doves and the larger pigeons, but the names are interchangeable.

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).

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

Variant forms of the same gene, occupying the same locus on homologous CHROMOSOMES, and governing the variants in production of the same gene product.

A plan for collecting and utilizing data so that desired information can be obtained with sufficient precision or so that an hypothesis can be tested properly.

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)

Predetermined sets of questions used to collect data - clinical data, social status, occupational group, etc. The term is often applied to a self-completed survey instrument.

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

Serum proteins that negatively regulate the cascade process of COMPLEMENT ACTIVATION. Uncontrolled complement activation and resulting cell lysis is potentially dangerous for the host. The complement system is tightly regulated by inactivators that accelerate the decay of intermediates and certain cell surface receptors.

The status during which female mammals carry their developing young (EMBRYOS or FETUSES) in utero before birth, beginning from FERTILIZATION to BIRTH.

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 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.

Strains of mice in which certain GENES of their GENOMES have been disrupted, or "knocked-out". To produce knockouts, using RECOMBINANT DNA technology, the normal DNA sequence of the gene being studied is altered to prevent synthesis of a normal gene product. Cloned cells in which this DNA alteration is successful are then injected into mouse EMBRYOS to produce chimeric mice. The chimeric mice are then bred to yield a strain in which all the cells of the mouse contain the disrupted gene. Knockout mice are used as EXPERIMENTAL ANIMAL MODELS for diseases (DISEASE MODELS, ANIMAL) and to clarify the functions of the genes.

The genetic constitution of the individual, comprising the ALLELES present at each GENETIC LOCUS.

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

A cell line generated from human embryonic kidney cells that were transformed with human adenovirus type 5.

The use of faith and spirit to cure disease.

Databases devoted to knowledge about specific genes and gene products.

An array of tests used to determine the toxicity of a substance to living systems. These include tests on clinical drugs, foods, and environmental pollutants.

A component of the CLASSICAL COMPLEMENT PATHWAY. C2 is cleaved by activated COMPLEMENT C1S into COMPLEMENT C2B and COMPLEMENT C2A. C2a, the COOH-terminal fragment containing a SERINE PROTEASE, combines with COMPLEMENT C4B to form C4b2a (CLASSICAL PATHWAY C3 CONVERTASE) and subsequent C4b2a3b (CLASSICAL PATHWAY C5 CONVERTASE).

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

A theorem in probability theory named for Thomas Bayes (1702-1761). In epidemiology, it is used to obtain the probability of disease in a group of people with some characteristic on the basis of the overall rate of that disease and of the likelihood of that characteristic in healthy and diseased individuals. The most familiar application is in clinical decision analysis where it is used for estimating the probability of a particular diagnosis given the appearance of some symptoms or test result.

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

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.

Works about pre-planned studies of the safety, efficacy, or optimum dosage schedule (if appropriate) of one or more diagnostic, therapeutic, or prophylactic drugs, devices, or techniques selected according to predetermined criteria of eligibility and observed for predefined evidence of favorable and unfavorable effects. This concept includes clinical trials conducted both in the U.S. and in other countries.

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

Concentrated pharmaceutical preparations of plants obtained by removing active constituents with a suitable solvent, which is evaporated away, and adjusting the residue to a prescribed standard.

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

The protection of animals in laboratories or other specific environments by promoting their health through better nutrition, housing, and care.

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)

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.

The strengthening of a conditioned response.

A large lobed glandular organ in the abdomen of vertebrates that is responsible for detoxification, metabolism, synthesis and storage of various substances.

A statistical technique that isolates and assesses the contributions of categorical independent variables to variation in the mean of a continuous dependent variable.

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.

Works about clinical trials that involve at least one test treatment and one control treatment, concurrent enrollment and follow-up of the test- and control-treated groups, and in which the treatments to be administered are selected by a random process, such as the use of a random-numbers table.

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.

The discipline concerned with using the combination of conventional ALLOPATHIC MEDICINE and ALTERNATIVE MEDICINE to address the biological, psychological, social, and spiritual aspects of health and illness.

Databases containing information about NUCLEIC ACIDS such as BASE SEQUENCE; SNPS; NUCLEIC ACID CONFORMATION; and other properties. Information about the DNA fragments kept in a GENE LIBRARY or GENOMIC LIBRARY is often maintained in DNA databases.

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

The giving of drugs, chemicals, or other substances by mouth.

Antibodies produced by a single clone of cells.

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

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.

Pathologic processes that affect patients after a surgical procedure. They may or may not be related to the disease for which the surgery was done, and they may or may not be direct results of the surgery.

The process of making a selective intellectual judgment when presented with several complex alternatives consisting of several variables, and usually defining a course of action or an idea.

Tumors or cancer of the human BREAST.

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 plant genus of the family BRASSICACEAE that contains ARABIDOPSIS PROTEINS and MADS DOMAIN PROTEINS. The species A. thaliana is used for experiments in classical plant genetics as well as molecular genetic studies in plant physiology, biochemistry, and development.

Any of various animals that constitute the family Suidae and comprise stout-bodied, short-legged omnivorous mammals with thick skin, usually covered with coarse bristles, a rather long mobile snout, and small tail. Included are the genera Babyrousa, Phacochoerus (wart hogs), and Sus, the latter containing the domestic pig (see SUS SCROFA).

A set of statistical methods used to group variables or observations into strongly inter-related subgroups. In epidemiology, it may be used to analyze a closely grouped series of events or cases of disease or other health-related phenomenon with well-defined distribution patterns in relation to time or place or both.

A loose confederation of computer communication networks around the world. The networks that make up the Internet are connected through several backbone networks. The Internet grew out of the US Government ARPAnet project and was designed to facilitate information exchange.

Histochemical localization of immunoreactive substances using labeled antibodies as reagents.

Characterization of an amphioxus paired box gene, AmphiPax2/5/8: developmental expression patterns in optic support cells, nephridium, thyroid-like structures and pharyngeal gill slits, but not in the midbrain-hindbrain boundary region. (1/9069)

On the basis of developmental gene expression, the vertebrate central nervous system comprises: a forebrain plus anterior midbrain, a midbrain-hindbrain boundary region (MHB) having organizer properties, and a rhombospinal domain. The vertebrate MHB is characterized by position, by organizer properties and by being the early site of action of Wnt1 and engrailed genes, and of genes of the Pax2/5/8 subfamily. Wada and others (Wada, H., Saiga, H., Satoh, N. and Holland, P. W. H. (1998) Development 125, 1113-1122) suggested that ascidian tunicates have a vertebrate-like MHB on the basis of ascidian Pax258 expression there. In another invertebrate chordate, amphioxus, comparable gene expression evidence for a vertebrate-like MHB is lacking. We, therefore, isolated and characterized AmphiPax2/5/8, the sole member of this subfamily in amphioxus. AmphiPax2/5/8 is initially expressed well back in the rhombospinal domain and not where a MHB would be expected. In contrast, most of the other expression domains of AmphiPax2/5/8 correspond to expression domains of vertebrate Pax2, Pax5 and Pax8 in structures that are probably homologous - support cells of the eye, nephridium, thyroid-like structures and pharyngeal gill slits; although AmphiPax2/5/8 is not transcribed in any structures that could be interpreted as homologues of vertebrate otic placodes or otic vesicles. In sum, the developmental expression of AmphiPax2/5/8 indicates that the amphioxus central nervous system lacks a MHB resembling the vertebrate isthmic region. Additional gene expression data for the developing ascidian and amphioxus nervous systems would help determine whether a MHB is a basal chordate character secondarily lost in amphioxus. The alternative is that the MHB is a vertebrate innovation. (+info)

The role of gene splicing, gene amplification and regulation in mosquito insecticide resistance. (2/9069)

The primary routes of insecticide resistance in all insects are alterations in the insecticide target sites or changes in the rate at which the insecticide is detoxified. Three enzyme systems, glutathione S-transferases, esterases and monooxygenases, are involved in the detoxification of the four major insecticide classes. These enzymes act by rapidly metabolizing the insecticide to non-toxic products, or by rapidly binding and very slowly turning over the insecticide (sequestration). In Culex mosquitoes, the most common organophosphate insecticide resistance mechanism is caused by co-amplification of two esterases. The amplified esterases are differentially regulated, with three times more Est beta 2(1) being produced than Est alpha 2(1). Cis-acting regulatory sequences associated with these esterases are under investigation. All the amplified esterases in different Culex species act through sequestration. The rates at which they bind with insecticides are more rapid than those for their non-amplified counterparts in the insecticide-susceptible insects. In contrast, esterase-based organophosphate resistance in Anopheles is invariably based on changes in substrate specificities and increased turnover rates of a small subset of insecticides. The up-regulation of both glutathione S-transferases and monooxygenases in resistant mosquitoes is due to the effects of a single major gene in each case. The products of these major genes up-regulate a broad range of enzymes. The diversity of glutathione S-transferases produced by Anopheles mosquitoes is increased by the splicing of different 5' ends of genes, with a single 3' end, within one class of this enzyme family. The trans-acting regulatory factors responsible for the up-regulation of both the monooxygenase and glutathione S-transferases still need to be identified, but the recent development of molecular tools for positional cloning in Anopheles gambiae now makes this possible. (+info)

Expression of the naturally occurring truncated trkB neurotrophin receptor induces outgrowth of filopodia and processes in neuroblastoma cells. (3/9069)

We have investigated the effects of the truncated trkB receptor isoform T1 (trkB.T1) by transient transfection into mouse N2a neuroblastoma cells. We observed that expression of trkB.T1 leads to a striking change in cell morphology characterized by outgrowth of filopodia and processes. A similar morphological response was also observed in SH-SY5Y human neuroblastoma cells and NIH3T3 fibroblasts transfected with trkB.T1. N2a cells lack endogenous expression of trkB isoforms, but express barely detectable amounts of its ligands, brain-derived neurotrophic factor (BDNF) and neurotrophin-4 (NT-4). The morphological change was ligand-independent, since addition of exogenous BDNF or NT-4 or blockade of endogenous trkB ligands did not influence this response. Filopodia and process outgrowth was significantly suppressed when full-length trkB.TK+ was cotransfected together with trkB.T1 and this inhibitory effect was blocked by tyrosine kinase inhibitor K252a. Transfection of trkB.T1 deletion mutants showed that the morphological response is dependent on the extracellular, but not the intracellular domain of the receptor. Our results suggest a novel ligand-independent role for truncated trkB in the regulation of cellular morphology. (+info)

Differential stability of the DNA-activated protein kinase catalytic subunit mRNA in human glioma cells. (4/9069)

DNA-dependent protein kinase (DNA-PK) functions in double-strand break repair and immunoglobulin [V(D)J] recombination. We previously established a radiation-sensitive human cell line, M059J, derived from a malignant glioma, which lacks the catalytic subunit (DNA-PKcs) of the DNA-PK multiprotein complex. Although previous Northern blot analysis failed to detect the DNA-PKcs transcript in these cells, we show here through quantitative studies that the transcript is present, albeit at greatly reduced (approximately 20x) levels. Sequencing revealed no genetic alteration in either the promoter region, the kinase domain, or the 3' untranslated region of the DNA-PKcs gene to account for the reduced transcript levels. Nuclear run-on transcription assays indicated that the rate of DNA-PKcs transcription in M059J and DNA-PKcs proficient cell lines was similar, but the stability of the DNA-PKcs message in the M059J cell line was drastically (approximately 20x) reduced. Furthermore, M059J cells lack an alternately spliced DNA-PKcs transcript that accounts for a minor (5-20%) proportion of the DNA-PKcs message in all other cell lines tested. Thus, alterations in DNA-PKcs mRNA stability and/or the lack of the alternate mRNA may result in the loss of DNA-PKcs activity. This finding has important implications as DNA-PKcs activity is essential to cells repairing damage induced by radiation or radiomimetric agents. (+info)

Selection and characterization of pre-mRNA splicing enhancers: identification of novel SR protein-specific enhancer sequences. (5/9069)

Splicing enhancers are RNA sequences required for accurate splice site recognition and the control of alternative splicing. In this study, we used an in vitro selection procedure to identify and characterize novel RNA sequences capable of functioning as pre-mRNA splicing enhancers. Randomized 18-nucleotide RNA sequences were inserted downstream from a Drosophila doublesex pre-mRNA enhancer-dependent splicing substrate. Functional splicing enhancers were then selected by multiple rounds of in vitro splicing in nuclear extracts, reverse transcription, and selective PCR amplification of the spliced products. Characterization of the selected splicing enhancers revealed a highly heterogeneous population of sequences, but we identified six classes of recurring degenerate sequence motifs five to seven nucleotides in length including novel splicing enhancer sequence motifs. Analysis of selected splicing enhancer elements and other enhancers in S100 complementation assays led to the identification of individual enhancers capable of being activated by specific serine/arginine (SR)-rich splicing factors (SC35, 9G8, and SF2/ASF). In addition, a potent splicing enhancer sequence isolated in the selection specifically binds a 20-kDa SR protein. This enhancer sequence has a high level of sequence homology with a recently identified RNA-protein adduct that can be immunoprecipitated with an SRp20-specific antibody. We conclude that distinct classes of selected enhancers are activated by specific SR proteins, but there is considerable sequence degeneracy within each class. The results presented here, in conjunction with previous studies, reveal a remarkably broad spectrum of RNA sequences capable of binding specific SR proteins and/or functioning as SR-specific splicing enhancers. (+info)

Alterations in the conserved SL1 trans-spliced leader of Caenorhabditis elegans demonstrate flexibility in length and sequence requirements in vivo. (6/9069)

Approximately 70% of mRNAs in Caenorhabditis elegans are trans spliced to conserved 21- to 23-nucleotide leader RNAs. While the function of SL1, the major C. elegans trans-spliced leader, is unknown, SL1 RNA, which contains this leader, is essential for embryogenesis. Efforts to characterize in vivo requirements of the SL1 leader sequence have been severely constrained by the essential role of the corresponding DNA sequences in SL1 RNA transcription. We devised a heterologous expression system that circumvents this problem, making it possible to probe the length and sequence requirements of the SL1 leader without interfering with its transcription. We report that expression of SL1 from a U2 snRNA promoter rescues mutants lacking the SL1-encoding genes and that the essential embryonic function of SL1 is retained when approximately one-third of the leader sequence and/or the length of the leader is significantly altered. In contrast, although all mutant SL1 RNAs were well expressed, more severe alterations eliminate this essential embryonic function. The one non-rescuing mutant leader tested was never detected on messages, demonstrating that part of the leader sequence is essential for trans splicing in vivo. Thus, in spite of the high degree of SL1 sequence conservation, its length, primary sequence, and composition are not critical parameters of its essential embryonic function. However, particular nucleotides in the leader are essential for the in vivo function of the SL1 RNA, perhaps for its assembly into a functional snRNP or for the trans-splicing reaction. (+info)

Mammalian staufen is a double-stranded-RNA- and tubulin-binding protein which localizes to the rough endoplasmic reticulum. (7/9069)

Staufen (Stau) is a double-stranded RNA (dsRNA)-binding protein involved in mRNA transport and localization in Drosophila. To understand the molecular mechanisms of mRNA transport in mammals, we cloned human (hStau) and mouse (mStau) staufen cDNAs. In humans, four transcripts arise by differential splicing of the Stau gene and code for two proteins with different N-terminal extremities. In vitro, hStau and mStau bind dsRNA via each of two full-length dsRNA-binding domains and tubulin via a region similar to the microtubule-binding domain of MAP-1B, suggesting that Stau cross-links cytoskeletal and RNA components. Immunofluorescent double labeling of transfected mammalian cells revealed that Stau is localized to the rough endoplasmic reticulum (RER), implicating this RNA-binding protein in mRNA targeting to the RER, perhaps via a multistep process involving microtubules. These results are the first demonstration of the association of an RNA-binding protein in addition to ribosomal proteins, with the RER, implicating this class of proteins in the transport of RNA to its site of translation. (+info)

Expression of novel alternatively spliced isoforms of the oct-1 transcription factor. (8/9069)

Analysis of the alternatively spliced isoforms of the human and mouse oct-1 genes, combined with their exon-intron structure, show a high level of evolutionary conservation between these two species. The differential expression of several oct-1 isoforms was examined by reverse transcription-polymerase chain reaction performed on the 3' region of the murine oct-1 cDNA. Variations in the relative levels and patterns of expression of the isoforms were found among different tissues. Three novel isoforms originating from the 3'-distal region of oct-1, were isolated and sequenced: Two were derived from testis, and one from myeloma cells. Splicing out of different exons as revealed in the structure of these isoforms results in reading frameshifts that presumably lead to the expression of shortened Oct-1 proteins, with distinct C-terminal tails. Altogether, six out of the eight known murine oct-1 isoforms may have distinct C-termini, implying that these multiple tails have different functional roles in cellular differentiation and physiology. (+info)

... , or alternative RNA splicing, or differential splicing, is an alternative splicing process during gene ... mRNAs undergoing alternative splicing and alternative splicing events or to study the functional impact of alternative splicing ... Research Group dealing with alternative Splicing issues and mis-splicing in human diseases Alternative Splicing of ion channels ... Wikimedia Commons has media related to Alternative splicing. A General Definition and Nomenclature for Alternative Splicing ...

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

... (ASAP) in computational biology was a database for alternative splicing data maintained ... Lee, Christopher; Atanelov, Levan; Modrek, Barmak; Xing, Yi (2003-01-01). "ASAP: the Alternative Splicing Annotation Project". ... analysis and comparative genomics of alternative splicing in 15 animal species". Nucleic Acids Res. England. 35 (Database issue ... AspicDB ECgene RNA splicing Kim, Namshin; Alekseyenko Alexander V; Roy Meenakshi; Lee Christopher (Jan 2007). "The ASAP II ...

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

Alternative Splicing Annotation Project AspicDB RNA splicing Koscielny, Gautier; Le Texier, Vincent; Gopalakrishnan, Chellappa ... "Alternative Splicing Database Project , EBI". www.ebi.ac.uk. Archived from the original on 2011-12-27. Retrieved 2020-03-04. ... The Alternative Splicing and Transcript Diversity database (ASTD) was a database of transcript variants maintained by the ... The Alternative Splicing and Transcript Diversity database". Genomics. United States. 93 (3): 213-20. doi:10.1016/j.ygeno. ...

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

The Human-transcriptome DataBase for Alternative Splicing (H-DBAS) is a database of alternatively spliced human transcripts ... Alternative splicing Takeda, Jun-ichi; Suzuki Yutaka; Nakao Mitsuteru; Kuroda Tsuyoshi; Sugano Sumio; Gojobori Takashi; ... alternative splicing database of completely sequenced and manually annotated full-length cDNAs based on H-Invitational". ... RNA splicing, All stub articles, Biological database stubs). ...

https://en.wikipedia.org/wiki/Human-transcriptome_DataBase_for_Alternative_Splicing

This phenomenon is then called alternative splicing. Alternative splicing can occur in many ways. Exons can be extended or ... DNA damage also has an impact on the splicing and alternative splicing of genes intimately associated with DNA repair. For ... The major spliceosome splices introns containing GU at the 5' splice site and AG at the 3' splice site. It is composed of the ... This type of splicing is termed canonical splicing or termed the lariat pathway, which accounts for more than 99% of splicing. ...

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

... (abbreviated sQTLs or splicing QTLs) are quantitative trait loci that regulate alternative ... Ongen H, Dermitzakis ET (October 2015). "Alternative Splicing QTLs in European and African Populations". American Journal of ... April 2016). "RNA splicing is a primary link between genetic variation and disease". Science. 352 (6285): 600-4. Bibcode: ... Takata A, Matsumoto N, Kato T (February 2017). "Genome-wide identification of splicing QTLs in the human brain and their ...

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

Alternative trans-splicing includes intragenic trans-splicing and intergenic trans-splicing. Intragenic trans-splicing involves ... Trans-splicing differs from cis-splicing in that there is no 5' splice site on the pre-mRNA. Instead the 5' splice site is ... splice site upstream. When the 5' outron in spliced, the 5' splice site of the spliced leader RNA is branched to the outron and ... trans-splicing can also be the mechanism behind certain oncogenic fusion transcripts. Spliced leader (SL) trans-splicing is ...

https://en.wikipedia.org/wiki/Trans-splicing

... splice site usage regulating alternative 3' splice site usage Myotonic dystrophy (MD) is most noticeably caused by inheriting ... "Alternative splicing and genetic diversity: silencers are more frequently modified by SNVs associated with alternative exon/ ... ESSs silence splice sites adjacent to them by interfering with the components of the core splicing complex, such as the snRNP's ... Exonic splicing silencers work by inhibiting the splicing of pre-mRNA strands or promoting exon skipping. The single stranded ...

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

Alternative splicing differs from RNA editing in that alternative splicing does not change the mRNA sequence like RNA editing ... Alternative splicing is a mechanism by which different proteins can be produced from a single gene by means of using ... This includes alternative splicing during transcription, whether the viral genome is segmented, the host range of viruses, ... Viruses may make use of alternative splicing solely to produce multiple proteins from a single pre-mRNA strand or for other ...

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

Alternative splicing produces ∆Elk1. This variant lacks part of the DNA-binding domain that allows interaction with SRF. On the ... Elk1 also interacts with BRCA1 splice variants, namely BRCA1a and BRCA1b. This interaction enhances BRCA1-mediated growth ... "c-Fos oncogene regulator Elk-1 interacts with BRCA1 splice variants BRCA1a/1b and enhances BRCA1a/1b-mediated growth ...

https://en.wikipedia.org/wiki/ELK1

Evidence for alternative splicing". J. Mol. Biol. 207 (3): 491-503. doi:10.1016/0022-2836(89)90459-2. PMID 2760922. Buvoli M, ... Buvoli M, Cobianchi F, Bestagno MG, Mangiarotti A, Bassi MT, Biamonti G, Riva S (1990). "Alternative splicing in the human gene ... and may modulate splice site selection. Multiple alternatively spliced transcript variants have been found for this gene but ... These variants have multiple alternative transcription initiation sites and multiple polyA sites. Post translational ...

https://en.wikipedia.org/wiki/HNRNPA1

Kelemen O, Convertini P, Zhang Z, Wen Y, Shen M, Falaleeva M, Stamm S (February 2013). "Function of alternative splicing". Gene ... Another mechanism for the correct regulation of gene expression is achieved through alternative splicing. This is a co- ... Latorre E, Mesonero JE, Harries LW (November 2019). "Alternative splicing in serotonergic system: Implications in ... including utilization of alternative splice acceptor sites, exon skipping, rare exon usage, and intron retention. There are a ...

https://en.wikipedia.org/wiki/5-HT2A_receptor

Alternative splicing, polyadenylation, and isoforms". The Journal of Biological Chemistry. 270 (34): 20112-22. doi:10.1074/jbc. ... Multiple alternatively spliced variants, encoding the same protein, have been found for this gene. Cluster of differentiation ...

https://en.wikipedia.org/wiki/Fucosyltransferase_3

Alternative splicing of transcription products". The Journal of Biological Chemistry. 272 (28): 17843-50. doi:10.1074/jbc. ... Several alternatively spliced transcript variants, some of which encode distinct isoforms, have been identified. Additional ... "Multi-forms of human MTH1 polypeptides produced by alternative translation initiation and single nucleotide polymorphism". ...

https://en.wikipedia.org/wiki/2-hydroxy-dATP_diphosphatase

Alternative splicing, polyadenylation, and isoforms". J. Biol. Chem. 270 (34): 20112-22. doi:10.1074/jbc.270.34.20112. PMID ... 2004). "Activity and tissue distribution of splice variants of alpha6-fucosyltransferase in human embryogenesis". Glycobiology ... large-scale identification and characterization of putative alternative promoters of human genes". Genome Res. 16 (1): 55-65. ...

https://en.wikipedia.org/wiki/FUT6

Teplova M, Patel DJ (December 2008). "Structural insights into RNA recognition by the alternative-splicing regulator ... Muscleblind Like Splicing Regulator 1 (MBNL1) is an RNA splicing protein that in humans is encoded by the MBNL1 gene. It has a ... The repressive function of Human MBNL1 by sequestering at normal splice sites has been shown to lead to RNA-splicing defects ... autoregulate alternative splicing of the MBNL1 pre-mRNA transcript. The founding member of the human MBNL family of proteins ...

https://en.wikipedia.org/wiki/MBNL1

Alternative splicing, polyadenylation, and isoforms". The Journal of Biological Chemistry. 270 (34): 20112-22. doi:10.1074/jbc. ...

https://en.wikipedia.org/wiki/FUT5

Kim N; Lee C (2008). Bioinformatics detection of alternative splicing. Methods in Molecular Biology. Vol. 452. pp. 179-97. doi: ... can be aligned to a sequenced genome to find where there are genes and get information about alternative splicing and RNA ... BLAST was developed to provide a faster alternative to FASTA without sacrificing much accuracy; like FASTA, BLAST uses a word ... Optical computing approaches have been suggested as promising alternatives to the current electrical implementations, yet their ...

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

"Medical Definition of ALTERNATIVE SPLICING". Merriam-webster.com. Retrieved 20 December 2021. "UniProtKB - Q5SQI0 (ATAT_HUMAN ... ATAT1 presents seven different isoforms due to alternative splicing, a process which consists in the combination of exons ...

https://en.wikipedia.org/wiki/Alpha-tubulin_N-acetyltransferase

Lareau LF, Green RE, Bhatnagar RS, Brenner SE (June 2004). "The evolving roles of alternative splicing". Current Opinion in ... In 2022, it was discovered that aminoacyl-trna synthetases may incorporate alternative amino acids during shortages of their ...

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

Woodley L, Valcárcel J (Oct 2002). "Regulation of alternative pre-mRNA splicing". Briefings in Functional Genomics & Proteomics ... the mutant pre-mRNA and the therapeutic pre-trans-splicing molecule carrying the wild-type sequence are spliced together to ... masking exonic splicing enhancer sequences and therefore preventing binding of the splicing machinery and therefore resulting ... Wally V, Murauer EM, Bauer JW (Aug 2012). "Spliceosome-mediated trans-splicing: the therapeutic cut and paste". The Journal of ...

https://en.wikipedia.org/wiki/Myosin_binding_protein_C,_cardiac

Alternative splicing occurs for this gene; however, the full-length nature of all transcript variants has not yet been ...

https://en.wikipedia.org/wiki/IHPK1

... others may be expressed in soluble form through alternative splicing. Like the similar KIR family, LILR genes are found in the ... "Extensive Alternative Splicing of KIR Transcripts". Frontiers in Immunology. 9: 2846. doi:10.3389/fimmu.2018.02846. PMC 6288254 ... as well as in alternative splicing. This family has undergone significant diversification in primate lineages. The leukocyte ...

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

Alternative splicing results in multiple variants. [provided by RefSeq, Jul 2017]. GRCh38: Ensembl release 89: ENSG00000186487 ...

https://en.wikipedia.org/wiki/MYT1L

This gene undergoes extensive alternative splicing; although ten transcript variants have been described, the full length ... Functional diversity of GIT2 through alternative splicing". The Journal of Biological Chemistry. 275 (29): 22373-80. doi: ...

https://en.wikipedia.org/wiki/GIT2

Alternative splicing Alternative Splicing Annotation Project AspicDB ChimerDB TassDB Kim, Pora; Kim Namshin; Lee Younghee; Kim ... ECgene in computational biology is a database of genomic annotations taking alternative splicing events into consideration. ... genome annotation for alternative splicing". Nucleic Acids Res. England. 33 (Database issue): D75-9. doi:10.1093/nar/gki118. ... RNA splicing, Gene expression, All stub articles, Biological database stubs). ...

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

Alternative splicing results in transcript variants. The LRRs and NTF2-like domains are required for export activity. The ... "Multipotent genetic suppression of retrotransposon-induced mutations by Nxf1 through fine-tuning of alternative splicing". PLOS ... is a component of the splicing-dependent exon-exon junction complex". The EMBO Journal. 20 (22): 6424-33. doi:10.1093/emboj/ ...

https://en.wikipedia.org/wiki/NXF1

Alternative splicing occurs for this gene; however, the full-length nature of all transcript variants has not yet been ...

https://en.wikipedia.org/wiki/TCEAL4

Barta, Andrea; Schumperli, Daniel (2010). "Editorial on alternative splicing and disease". RNA Biology. 7 (4): 388-389. doi: ... the ribosomes would try to bind to both the un-spliced primary RNA transcript and the spliced mRNA, which would result in a ... "Human Splicing Finder: an online bioinformatics tool to predict splicing signals". Nucleic Acids Research. 37 (9): e67. doi: ... and that would define the splice junctions. Senapathy found that almost all splice junctions in eukaryotic genes contained stop ...

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

Alternative splicing generates 2 transcript variants. GRCh38: Ensembl release 89: ENSG00000174233 - Ensembl, May 2017 GRCm38: ...

https://en.wikipedia.org/wiki/ADCY6

"EGFR mutation-induced alternative splicing of Max contributes to growth of glycolytic tumors in brain cancer". Cell Metabolism ...

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

DNA-templated transcription, with some alternative splicing mechanism is the method of transcription. The virus exits the host ...

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

NFI-X3, a splice variant of NFIX, regulates Glial fibrillary acidic protein and YKL-40 in astrocytes. Nfix has been shown to ... is generated by alternative RNA processing". J. Biol. Chem. 272 (16): 10739-10745. doi:10.1074/jbc.272.16.10739. PMID 9099724. ... Apt D, Liu Y, Bernard HU (1994). "Cloning and functional analysis of spliced isoforms of human nuclear factor I-X: interference ...

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

Alternative splicing of this gene results in transcript variants encoding different isoforms. GABRG2 has been shown to interact ... Kananura C, Haug K, Sander T, Runge U, Gu W, Hallmann K, Rebstock J, Heils A, Steinlein OK (July 2002). "A splice-site mutation ...

https://en.wikipedia.org/wiki/Gamma-aminobutyric_acid_receptor_subunit_gamma-2

... slashing hardcore spliced to a twinkly chorus, unfamiliar bedfellows only seeking coexistence." Kerrang! included Handsome on a ... "incredible potential but did not quite fit anywhere within the worlds of alternative, metal and the nightmarish arrival of nu ...

https://en.wikipedia.org/wiki/Handsome_(Handsome_album)

Some of these are believed to affect the shape of nucleic acids (see for example RNA self-splicing), but this is only sometimes ... and the square brackets indicate an alternative (see below for further details about notation). Usually, however, the first ...

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

Stoss O, Schwaiger FW, Cooper TA, Stamm S (1999). "Alternative splicing determines the intracellular localization of the novel ... "Alternative splicing determines the intracellular localization of the novel nuclear protein Nop30 and its interaction with the ... splicing factor SRp30c". J. Biol. Chem. 274 (16): 10951-62. doi:10.1074/jbc.274.16.10951. PMID 10196175. ... nuclear protein Nop30 and its interaction with the splicing factor SRp30c". J. Biol. Chem. 274 (16): 10951-62. doi:10.1074/jbc. ...

https://en.wikipedia.org/wiki/NOL3

Several alternatively spliced transcript variants encoding different isoforms exist. GRCh38: Ensembl release 89: ... Large-scale identification and characterization of putative alternative promoters of human genes". Genome Res. 16 (1): 55-65. ...

https://en.wikipedia.org/wiki/EPS8L1

... encoded by six different alternative splices of its gene, CMTM5; CMTM5-v1 is the most studied of these isoforms. The CMTM5 gene ...

https://en.wikipedia.org/wiki/CKLF-like_MARVEL_transmembrane_domain-containing_5

DNA-templated transcription, with some alternative splicing mechanism is the method of transcription. The virus exits the host ...

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

The protein encoded by this gene is involved in mRNA splicing and may play a role in site selection in alternative splicing. ... Li J, Hawkins IC, Harvey CD, Jennings JL, Link AJ, Patton JG (November 2003). "Regulation of alternative splicing by SRrp86 and ... Tran Q, Roesser JR (February 2003). "SRp55 is a regulator of calcitonin/CGRP alternative RNA splicing". Biochemistry. 42 (4): ... Nagel RJ, Lancaster AM, Zahler AM (January 1998). "Specific binding of an exonic splicing enhancer by the pre-mRNA splicing ...

https://en.wikipedia.org/wiki/SFRS6

The song became a number-one hit on two other Billboard charts: the Adult Alternative Songs chart and the Adult Top 40. On the ... Retrospectively, Raymond Cummings of popular culture website Splice Today gave the song a negative review, referring to is as ... "Adult Alternative Airplay: The Week of May 25, 2002". Billboard. May 25, 2002. Archived from the original on August 24, 2021. ... Cummings, Raymond (March 27, 2013). "Sheryl Crow's "Soak Up the Sun": Just Shoot Me". Splice Today. Archived from the original ...

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

Alternative splicing has been identified, with observed variation resulting in the presence or absence of domains. In addition ... splicing occurs in the 5' UTR but transcripts including these variations have not been described completely. ENSG00000273572 ... Large-scale identification and characterization of putative alternative promoters of human genes". Genome Res. 16 (1): 55-65. ...

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

Alternative splicing of this gene results in multiple transcript variants. A related pseudogene has been identified on ...

https://en.wikipedia.org/wiki/N6AMT1

An alternative splice variant has been described but its full length sequence has not been determined. FMNL1 has been shown to ...

https://en.wikipedia.org/wiki/FMNL1

... as a result of alternative splicing. This contributes to the evolutionary difference between the nervous system of mammals and ... "An alternative splicing event amplifies evolutionary differences between vertebrates". Science. 349 (6250): 868-873. Bibcode: ... "The MicroRNA miR-124 promotes neuronal differentiation by triggering brain-specific alternative pre-mRNA splicing". Molecular ... Alternatively spliced transcript variants encoding different isoforms have been described. In brains of mammals, transcripts ...

https://en.wikipedia.org/wiki/PTBP1

Alternative splicing results in multiple transcript variants. Read-through transcription also exists between this gene and the ... identification of novel MAGE-A10 splice variants". Clin. Cancer Res. 10 (17): 5708-16. doi:10.1158/1078-0432.CCR-04-0468. PMID ...

https://en.wikipedia.org/wiki/MAGEA10

DNA-templated transcription, with some alternative splicing mechanism is the method of transcription. The virus exits the host ...

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

There are two isoforms of the gene transcript that exist by alternative splicing, and one gene precursor. SLF2 (FAM178A) is an ... The molecular weight of the protein is 76.5 kilodaltons, and the isoelectric point is 5.47.The gene has 6 transcript splice ... Gene: FAM178B (ENSG00000168754) - Splice variants - Homo sapiens - Ensembl genome browser 95. (n.d.). Retrieved February 25, ... 2019, from http://useast.ensembl.org/Homo_sapiens/Gene/Splice?db=core;g=ENSG00000168754;r=2:96875882-96986592 Bipolar disorder ...

https://en.wikipedia.org/wiki/FAM178B

DNA-templated transcription, with some alternative splicing mechanism is the method of transcription. The virus exits the host ...

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

... pseudogenes and alternative-splice variants". Pharmacogenetics. 14 (1): 1-18. doi:10.1097/00008571-200401000-00001. PMID ...

https://en.wikipedia.org/wiki/CYP2B6

Additionally, some proteome samples of vertebrates have a large number of paralogs, and alternative splicing in higher ... Targeted proteomics using SRM and data-independent acquisition methods are often considered alternatives to shotgun proteomics ...

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

Homma K, Kikuno RF, Nagase T, Ohara O, Nishikawa K (November 2004). "Alternative splice variants encoding unstable protein ...

https://en.wikipedia.org/wiki/TIAF1

Mu W, Cheng Q, Yang J, Burt DR (2002). "Alternative splicing of the GABA(A) receptor alpha 4 subunit creates a severely ...

https://en.wikipedia.org/wiki/GABRA4

SON is required for genome stability by ensuring the efficiency of RNA splicing of weak constitutive and alternative splice ... Aberrant SON-mediated RNA splicing results from the accumulation of mis-spliced transcripts. The mis-spliced RNA products are ... The presence of these domains is necessary for SON to mediate constitutive and alternative splicing. The RS-rich domain serves ... Juan-Mateu, Jonàs; Villate, Olatz; Eizirik, Décio L (May 2016). "MECHANISMS IN ENDOCRINOLOGY: Alternative splicing: the new ...

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

January 2009). "CD96 interaction with CD155 via its first Ig-like domain is modulated by alternative splicing or mutations in ... Alternative splicing generates multiple transcript variants encoding distinct isoforms. [provided by RefSeq, Jan 2016]. GRCh38 ... It may also function in antigen presentation[citation needed]. Alternative splicing occurs at this locus and two transcript ...

https://en.wikipedia.org/wiki/CD96

He has since established himself as an alternative singer-songwriter, and continues to release solo albums, as well as perform ... "The Allure of the Obsolete". Splice Today. Retrieved 22 October 2016. "Chris Connelly Interview". Art Interviews.com. Retrieved ...

https://en.wikipedia.org/wiki/Chris_Connelly_(musician)

Krick R, Jakubiczka S, Arnemann J (2003). "Expression, alternative splicing and haplotype analysis of transcribed testis ...

https://en.wikipedia.org/wiki/TSPY1

Alternative splicing results in multiple transcript variants encoding different isoforms. SF3B1 has been shown to interact with ... This gene encodes subunit 1 of the splicing factor 3b protein complex. Splicing factor 3b, together with splicing factor 3a and ... Splicing factor 3b is also a component of the minor U12-type spliceosome. The carboxy-terminal two-thirds of subunit 1 have 22 ... "Entrez Gene: SF3B1 splicing factor 3b, subunit 1, 155kDa". Ajuh P, Kuster B, Panov K, Zomerdijk JC, Mann M, Lamond AI (December ...

https://en.wikipedia.org/wiki/SF3B1

Li J, Hawkins IC, Harvey CD, Jennings JL, Link AJ, Patton JG (Nov 2003). "Regulation of alternative splicing by SRrp86 and its ... Alternatively spliced transcript variants encoding different isoforms have been identified but their biological nature has not ... and other hnRNP G proteins interact with Tra2beta and affect splicing". Human Molecular Genetics. 9 (5): 685-94. doi:10.1093/ ...

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

Among the DEAS genes, the least and most abundant alternative splicing types were alternative 5′ splice site (5.23%) and exon ... We investigated the alternative splicing pattern in the posterior kidney of brown trout during PKD. Results: RNA-seq data were ... Genome-wide alternative splicing profile in the posterior kidney of brown trout (Salmo trutta) during proliferative kidney ... Sudhagar, A., El-Matbouli, M., & Kumar, G. (2022). Genome-wide alternative splicing profile in the posterior kidney of brown ...

https://www.mendeley.com/catalogue/9b01fec6-2050-38f6-aed3-195fa4c66aa4/

... causing alternative pre-mRNA splicing by intron 3 retention. Furthermore, the aberrant AIRE transcript was identified in a ... Minigene splicing analysis and subsequent cDNA sequencing revealed that the AIRE mutation potentially compromised the ... Therefore, our study represents the first functional characterization of the alternatively spliced AIRE mutation that may ... In silico splice-site prediction and minigene analysis were carried out to study the potential pathological consequence. ...

https://journals.plos.org/plosone/article?id=10.1371/journal.pone.0053981

Alternative Splicing in Tumors: Detection and Interpretation. Add to your list(s) Download to your calendar using vCal ... Then I will briefly discuss some of the additional issues which arise when we seek to enumerate such alternative splicing ... University of Cambridge , Talks.cam , Statistics , Alternative Splicing in Tumors: Detection and Interpretation ... Next I will outline the way in which we use such data in our attempts to identify exon-tumor combinations exhibiting splicing ...

http://talks.cam.ac.uk/talk/index/10678

Exon-exon junction spanning peptides provide direct evidence for the translation of specific splice isoforms and are critical ... Alternative splicing dramatically increases transcriptome complexity but its contribution to proteome diversity remains ... Detection of Proteome Diversity Resulted from Alternative Splicing is Limited by Trypsin Cleavage Specificity Mol Cell ... Alternative splicing dramatically increases transcriptome complexity but its contribution to proteome diversity remains ...

https://pubmed.ncbi.nlm.nih.gov/29222161/

Tool for the detection and quantification of alternative splicing events from RNA-Seq data. - ... This README describes the software SplAdder, short for Splicing Adder, a toolbox for alternative splicing analysis based on RNA ... augments the splicing graph with additional information extracted from the read data, extracts alternative splicing events from ... Tool for the detection and quantification of alternative splicing events from RNA-Seq data. ...

https://github.com/ratschlab/spladder

Results: We describe variable window binding - a mechanism used for mutually exclusive alternative splicing by which a ... Conclusion: On the basis of comparative sequence analysis, we propose efficient biologic mechanisms of alternative splicing of ... in the sense that only one exon is included in the mature mRNA out of a cluster of alternative choices, often arranged in a ... Genes of advanced organisms undergo alternative splicing, which can be mutually exclusive, ...

https://academiccommons.columbia.edu/doi/10.7916/D8Q23XQZ

Rapid and dynamic alternative splicing impacts the arabidopsis cold response transcriptome. Title. Rapid and dynamic ... Printed from /publications/rapid-and-dynamic-alternative-splicing-impacts-arabidopsis-cold-response-transcriptom-0 on 03/12/22 ...

https://www.hutton.ac.uk/publications/rapid-and-dynamic-alternative-splicing-impacts-arabidopsis-cold-response-transcriptom-0

Then, splicing correlation network was constructed based on these AS events and associated splicing factors. LASSO regression ... An AS correlation network, including 54 AS events and 94 splicing factors, was constructed, and further functional enrichment ... Alternative splicing (AS), one of the main post-transcriptional biological regulation mechanisms, plays a key role in the ... Cancer-associated SF3B1 mutations affect alternative splicing by promoting alternative branchpoint usage. Nat Commun. 2016;7(1 ...

https://bmccancer.biomedcentral.com/articles/10.1186/s12885-021-08681-z

Triple-negative breast cancer cells respond to T cells severely at the alternative splicing layer ... Triple-negative breast cancer cells respond to T cells severely at the alternative splicing layer ... Triple-negative breast cancer cells respond to T cells severely at the alternative splicing layer ... Triple-negative breast cancer cells respond to T cells severely at the alternative splicing layer. Lina Zhao, Xi Yang, Chun ...

http://ejbiotechnology.info/index.php/ejbiotechnology/article/view/2021.01.001

Alternative splicing regulation of the epithelial sodium channel (ENaC) in Dahl rats. Description. Title: Alternative splicing ... Two coding (a and b) and two non coding (c and d) alpha ENaC alternatively spliced forms were identified whose mRNA levels were ... To examine the putative biological function of alpha ENaC alternatively spliced forms when co-expressed with alpha ENaC-wt. The ... kidney is associated with alternatively spliced forms, and their corresponding mRNA levels, should they exist, in Dahl S versus ...

https://ruor.uottawa.ca/handle/10393/30135

Alternative pre-mRNA splicing (AS) supports the dynamic and regulated diversification of cells by allowing the production of ... Abstract P231: Multigenomic characterization of context-dependent alternative splicing in normal and neoplastic cells Elizabeth ... Multigenomic characterization of context-dependent alternative splicing in normal and neoplastic cells [abstract]. In: ... Multigenomic characterization of context-dependent alternative splicing in normal and neoplastic cells. Mol Cancer Ther 1 ...

https://aacrjournals.org/mct/article/20/12_Supplement/P231/676105/Abstract-P231-Multigenomic-characterization-of?searchresult=1

... that could identify internal alternative splicing in circRNA and compare differential circRNA splicing events between different ... Furthermore, cancer-specific alternative splicing of circRNA is less likely to be identified. Here, we proposed a de novo ... However, the internal structure of circRNA is difficult to determine due to alternative splicing that occurs in its exons and ... This study is the first comprehensive view of cancer-specific circRNA alternative splicing, which could contribute ...

https://molecular-cancer.biomedcentral.com/articles/10.1186/s12943-019-0996-0

Alternative splicing (AS) is the mechanism by which exons of a single gene can be spliced in various combinations to encode a ... Ultraconserved elements are associated with homeostatic control of splicing regulators by alternative splicing and nonsense- ... Temporal requirement of the alternative-splicing factor Sfrs1for the survival of retinal neurons Rahul N. Kanadia, Rahul N. ... the current investigation focuses on understanding the role of an alternative-splicing factor (ASF) called splicing factor ...

https://journals.biologists.com/dev/article/135/23/3923/64844/Temporal-requirement-of-the-alternative-splicing

This ensemble machine learning approach combines regional splicing constraint with multiple per-nucleotide alternative splicing ... Several existing tools predict the likelihood that a genetic variant causes alternative splicing. We sought to extend such ... Our metric combines genetic variation in the Genome Aggregate Database with alternative splicing predictions from SpliceAI to ... A particularly challenging barrier to diagnosis is identifying variants that cause deleterious alternative splicing at intronic ...

https://bmcbioinformatics.biomedcentral.com/articles/10.1186/s12859-022-05041-x

... is expressed by read-through alternative splicing. Specific feline A3 proteins selectively inactivated only defined genera of ... Functions, structure, and read-through alternative splicing of feline APOBEC3 genes. Carsten Münk, Thomas Beck, Jörg Zielonka, ... is expressed by read-through alternative splicing. Specific feline A3 proteins selectively inactivated only defined genera of ...

https://publikationen.ub.uni-frankfurt.de/frontdoor/index/index/searchtype/authorsearch/author/Marion+Battenberg/start/0/rows/10/author_facetfq/O%27Brien%2C+Stephen+J./docId/5626

High-Resolution Expression Map of the Arabidopsis Root Reveals Alternative Splicing and lincRNA Regulation. ... High-Resolution Expression Map of the Arabidopsis Root Reveals Alternative Splicing and lincRNA Regulation. Journal Article ( ... Coordinated alternative splicing across developmental stages pointed to a role in regulating differentiation. Consistent with ... Comparisons across cell types revealed that alternative splicing tends to remove parts of coding regions from a longer, major ...

https://scholars.duke.edu/display/pub1157447

An alternative splice variant of human αA-crystallin modulates the oligomer ensemble and the chaperone activity of α- ... Thus, alternative mRNA splicing of human αA-crystallin leads to an additional, formerly not characterized αA-crystallin species ... Here, we analyzed a previously uncharacterized, alternative splice variant (isoform 2) of human αA-crystallin with an exchanged ...

https://cipsm.de/publications/research-area-b/an-alternative-splice-variant-of-human-a-crystallin-modulates-the-oligomer-ensemble-and-the-chaperone-activity-of-crystallins/

We use cookies to ensure that we give you the best experience on our website. If you click Accept all cookies well assume that you are happy to receive all cookies and you wont see this message again. If you click Reject all non-essential cookies only necessary cookies providing core functionality such as security, network management, and accessibility will be enabled. Click Find out more for information on how to change your cookie settings. ...

https://www.jenner.ac.uk/publications/172053

New Developments in Alternative Splicing Research. $179.00. Select options. Sort by popularity. Sort by latest. Sort by price: ...

https://novapublishers.com/product-tag/9781628087208/

... w will reveal the role of splicing-factor defects in cardiac or neurological disorders, cancer and more. ... Following transcription, a process called alternative RNA splicing enables the creation of different spliced mRNA versions that ... Splicing factors are RNA-binding proteins that regulate splicing, and manipulating splicing-factor levels could lead to ... A Jackson Laboratory (JAX) research team led by Olga Anczuków-Camarda, Ph.D.Investigates how alternative RNA splicing ...

https://www.jax.org/news-and-insights/2020/August/correcting-splicing-factor-defects-in-disease

... derived neurons well represent the diversity of NRXN1α alternative splicing observed in the human brain, cataloguing 123 high- ... NRXN1 undergoes extensive alternative splicing, and non-recurrent heterozygous deletions in NRXN1 are strongly associated with ... Targeted combinatorial alternative splicing generates brain region-specific repertoires of neurexins. Neuron 84, 386-398 (2014 ... An alternative splicing switch shapes neurexin repertoires in principal neurons versus interneurons in the mouse hippocampus. ...

https://www.nature.com/articles/s41588-019-0539-z?error=cookies_not_supported&code=cc843ae7-bfd9-4085-918e-2c292217af24

It has been observed that alternative splicing of the DCC can affect its activity and that alternative splicing of DCC can be ... In this way, we determined that 29 of 35 CRC cell lines had altered splice patterns, indicating the alternative splicing may be ... The Association of DCC mRNA Alternative Splicing with Colorectal Cancer Public Deposited ... we sought to determine the association of alternative splicing of the DCC with colorectal cancer in cells without the deletion ...

https://scholar.colorado.edu/concern/undergraduate_honors_theses/1831ck330

... shows heterogeneity in molecular expression as a result of post-translational modification as well as alternative splicing of ... The use of exon-specific primers allowed detection of multiple alternatively spliced mRNA species involving expression of at ... Taken together, these findings demonstrate that the mouse expresses multiple variably spliced CD44 isoforms and that expression ... Interestingly, different mouse tissues, including lymphoid cells, showed unique patterns of alternative CD44 mRNA in Southern ...

https://www.imm.ox.ac.uk/publications/102765

The encoded protein functions as a pre-mRNA splicing factor. There is a pseudogene for this gene on chromosome 7. Alternative ... serine/arginine-rich splicing factor 8. Names. SR splicing factor 8. pre-mRNA-splicing factor SRP46. splicing factor, arginine/ ... Increased expression of splicing factor SRp20 mRNA in bipolar disorder patients. Watanuki T, et al. J Affect Disord, 2008 Sep. ... Serine/arginine-rich splicing factor 8 (SRSF8) is identified to interact with HIV-1 Tat mutant Nullbasic in HeLa cells by LC MS ...

https://www.ncbi.nlm.nih.gov/gene/10929

Evidence of alternative splicing in gene expression. Yau jan Chyan, Susan Ackerman, Nancy S. Shepherd, O. Wesley Mcbride, ... Evidence of alternative splicing in gene expression",. abstract = "DNA polymerase β (β-pol) is a single-copy gene that is ... Evidence of alternative splicing in gene expression. Nucleic acids research. 1994 Jul 25;22(14):2719-2725. doi: 10.1093/nar/ ... Evidence of alternative splicing in gene expression. In: Nucleic acids research. 1994 ; Vol. 22, No. 14. pp. 2719-2725. ...

https://researchexperts.utmb.edu/en/publications/the-human-dna-polymerase-%CE%B2-gene-structure-evidence-of-alternative

Drosophila melanogaster Myosin 7B gene with alternatively spliced exons. Organism. Drosophila melanogaster. ...

https://webscipio.org/help/alternative_splicing

Alternative splicing is emerging as a major mechanism for the expansion of the transcriptome and proteome diversity, ... ASPicDB: a database of annotated transcript and protein variants generated by alternative splicing. Martelli, PL;DAntonio, M; ... Alternative splicing is emerging as a major mechanism for the expansion of the transcriptome and proteome diversity, ... 2011). ASPicDB: a database of annotated transcript and protein variants generated by alternative splicing. NUCLEIC ACIDS ...

https://boa.unimib.it/handle/10281/26185

... via promoting alternative intronic retention splicing and splice-dependent intron-retention nonsense mediated decay (Han et al ... For example, the lack of 53BP1 foci may be due to hypoxia-induced transcriptional and alternative splicing of TP53BP1 (Memon et ... 2017). Hypoxia is a key driver of alternative splicing in human breast cancer cells. Sci. Rep. 7, 1-17. ... Another driving force of genomic instability is the hypoxia-induced alternative splicing of DDR and DNA repair genes (Salas- ...

https://www.frontiersin.org/articles/10.3389/fcell.2021.626229/full

Transcriptome profiling reveals transcriptional and alternative splicing regulation in the early embryonic development of hair ... As an alternative strategy, to ensure we had not missed any known rare diseases or skin phenotype associations, we also ...

https://www.nature.com/articles/ncomms4540?error=cookies_not_supported

Alternative splicing. A biological process in which introns are removed from RNA in different combinations to produce different ... The alternative hypothesis is contradictory to H0 and is judged the more plausible claim when H0 is rejected. ... Alternative Hypothesis or H(a). The claim in a significance test that we are trying to gather evidence for - the researchers ... The emphasis on Eastern religion, alternative states of reality, hedonism, and nature suggests that these poets were seeking to ...

https://www.learner.org/glossary/constructing-social-reality/

Among the DEAS genes, the least and most abundant alternative splicing types were alternative 5′ splice site (5.23%) and exon skipping (70.59%), respectively. (mendeley.com)
In this talk I will discuss using the Affymetrix GeneChip® Human Exon and Human Gene 1.0 ST arrays for the detection of genes spliced differently in some tumors in comparison with others. (cam.ac.uk)
Background: Genes of advanced organisms undergo alternative splicing, which can be mutually exclusive, in the sense that only one exon is included in the mature mRNA out of a cluster of alternative choices, often arranged in a tandem array. (columbia.edu)
Alternative splicing (AS) is a common phenomenon in eukaryotes and occurs in approximately 90% of human genes [ 14 ]. (biomedcentral.com)
Alternative pre-mRNA splicing (AS) supports the dynamic and regulated diversification of cells by allowing the production of multiple distinct proteins from individual genes. (aacrjournals.org)
Multi-omics data integration revealed sensitivity to cirtuvivint was associated with alterations in splicing genes and that drug-induced ASEs were significantly associated with disease-promoting biology across lineage and oncogenic driver contexts. (aacrjournals.org)
Alternative splicing is the primary mechanism by which a limited number of protein-coding genes can generate proteome diversity. (biologists.com)
This ensemble machine learning approach combines regional splicing constraint with multiple per-nucleotide alternative splicing scores to guide the prediction of deleterious splicing variants in protein-coding genes. (biomedcentral.com)
Whether joining together pieces of film or our genes, splicing controls how information is conveyed. (jax.org)
Unproductive splicing of SR genes associated with highly conserved and ultraconserved DNA elements. (nih.gov)
Human genes undergo various patterns of pre-mRNA splicing across different tissues. (biomedcentral.com)
According to studies using large-scale expressed sequence tags (EST), as high as 60% of human genes are estimated to undergo alternative splicing [ 1 ]. (biomedcentral.com)
Study Design: Inferring a plausible statistical model of exon combinatorics from the annotated models of human genes during RNA splicing. (who.int)
The power-law behavior of exons during RNA splicing gives the unique characteristics to human genes. (who.int)
To determine whether alternative splicing played a role in adult muscle maintenance, we disrupted the process in adult mice by knocking out the genes Rbfox1 and Rbfox2 only in skeletal muscles. (besthealtharticle.com)
Two weeks after knocking out the genes Rbfox1 and Rbfox2, hundreds of other genes altered their expression and other genes their alternative splicing, including the capn3 gene, which switched splicing to produce an active form of a protease, an enzyme that degrades proteins. (besthealtharticle.com)
For protein-encoding genes the splicing reactions are catalyzed by an RNA/protein complex called a spliceosome. (blogspot.com)
Specifically, we found that differentially spliced genes (DSGs) and differentially expressed genes (DEG) share very limited overlapping under all kinds of stresses, suggesting that gene expression regulation and AS seemed to play independent roles in response to stresses. (bvsalud.org)
Availability of the complete genomes of 34 invertebrates, together with transcriptomes and ESTs, allowed us to systematically investigate the gene structure and alternative splicing of FABP genes over a wide range of phyla. (nottingham.ac.uk)
Example code to retrieve Alternative Splicing events from a set of genes. (ebi.ac.uk)
Beyond Genes: Inclusion of Alternative Splicing and Alternative Polyadenylation to Assess the Genetic Architecture of Predisposition to Voluntary Alcohol Consumption in Brain of the HXB/BXH Recombinant Inbred Rat Panel. (ucdenver.edu)
They say, for example, that genes don't always code just a single protein but get spliced up into different versions. (nationalgeographic.com)

Results: We describe 'variable window binding' - a mechanism used for mutually exclusive alternative splicing by which a segment ('window') of a conserved nucleotide 'anchor' sequence upstream of the exon 6 cluster in the pre-mRNA of the fruitfly Dscam gene binds to one of the introns, thereby activating selection of the exon directly downstream from the binding site. (columbia.edu)
Conclusion: On the basis of comparative sequence analysis, we propose efficient biologic mechanisms of alternative splicing of the Drosophila Dscam gene that rely on the inherent structure of the pre-mRNA. (columbia.edu)
Two coding (a and b) and two non coding (c and d) alpha ENaC alternatively spliced forms were identified whose mRNA levels were elevated in Dahl R versus S rats. (uottawa.ca)
The CDC2-like kinases (CLKs) and dual-specificity tyrosine-regulated kinases (DYRKs) are thought to govern the efficiency and specificity of AS by directly phosphorylating serine/arginine-rich splicing factors (SRSFs) and thereby influencing pre-mRNA splice junction selection. (aacrjournals.org)
Early experiments estimated that about 15% of disease-causing point mutations affect pre-mRNA splicing, [ 26 ]. (biomedcentral.com)
Thus, alternative mRNA splicing of human αA-crystallin leads to an additional, formerly not characterized αA-crystallin species which is able to modulate the properties of the canonical ensemble of α-crystallin oligomers. (cipsm.de)
Following transcription, a process called alternative RNA splicing enables the creation of different spliced mRNA versions that, in turn, can produce proteins with different functions. (jax.org)
CD44 is a widely distributed cell surface glycoprotein which shows heterogeneity in molecular expression as a result of post-translational modification as well as alternative splicing of CD44 mRNA. (ox.ac.uk)
These observations have raised the possibility that structural modifications of CD44, including those resulting from alternatively spliced mRNA isoforms, are involved in the functional heterogeneity of CD44. (ox.ac.uk)
Interestingly, different mouse tissues, including lymphoid cells, showed unique patterns of alternative CD44 mRNA in Southern blotting analysis. (ox.ac.uk)
The use of exon-specific primers allowed detection of multiple alternatively spliced mRNA species involving expression of at least seven variable exons. (ox.ac.uk)
Cloning and sequencing of these PCR products revealed sequence identity with recently identified genomic CD44 sequences and confirmed that the PCR products correspond to mature mRNA expressing alternatively spliced CD44 exons. (ox.ac.uk)
The encoded protein functions as a pre-mRNA splicing factor. (nih.gov)
Increased expression of splicing factor SRp20 mRNA in bipolar disorder patients. (nih.gov)
See 10 reference mRNA sequence splice variants for the RHD gene. (nih.gov)
Alternative splicing of pre-mRNA is a major mechanism of diversifying the protein coding potential of eukaryotic genomes. (biomedcentral.com)
More complicated regulatory mechanisms involving the combination of large numbers of trans -acting RBPs (RNA binding proteins that bind to the cis -acting RNA elements to control pre-mRNA splicing) and cis -acting elements (binding sites of trans -acting RNA binding proteins) remain unclear and further studies are warranted. (biomedcentral.com)
Our findings suggest that PTK7 is evolutionarily distinct from other RPTKs, and that the alternative splicing of PTK7 mRNA may contribute to its diverse function in cell signaling. (elsevier.com)
The underlying genetic mechanism for differential mRNA splicing is an ancient intronic deletion [del(ctc)] within A3H haplotype II sequence. (uthscsa.edu)
More importantly, the introns are spliced out and the exon sequences are fused to form the mature mRNA. (blogspot.com)
In the publication entitled " Cartography of neurexin alternative splicing mapped by single-molecule long-read mRNA sequencing ," the scientists highlight the importance of understanding alternative splicing in neurexins. (pacb.com)
Alternative pre-mRNA processing is a central element of eukaryotic gene regulation. (umassmed.edu)
Schematic representation of the 2 human bocavirus 1 (HBoV1) mRNA PCR products, illustrating alternative splicing. (cdc.gov)
Interestingly, several species including one trematode, one nematode and four arthropods generated FABP mRNA variants via alternative splicing. (nottingham.ac.uk)
Several isoforms of hnRNP D protein have been found to occur due to alternative mRNA splicing (RNA SPLICING). (bireme.br)
A group of closely-related heterogeneous-nuclear ribonucleoproteins that are involved in pre-mRNA splicing. (bireme.br)

However, the internal structure of circRNA is difficult to determine due to alternative splicing that occurs in its exons and introns. (biomedcentral.com)
Alternative splicing (AS) is the mechanism by which exons of a single gene can be spliced in various combinations to encode a diverse set of proteins. (biologists.com)
Consequently, potential splicing variants lying within introns or exons are commonly ignored during clinical diagnosis. (biomedcentral.com)
We hypothesize that poison-exons play a critical role in maintaining a tight regulation of splicing-factor levels, which is necessary for normal cell functions," she says. (jax.org)
For instance, previous studies have reported that modulation in the relative concentrations of hnRNP A/B proteins and SR proteins can control both the alternative splice site choice and the inclusion/exclusion ratio of selected alternative exons [ 11 - 15 ]. (biomedcentral.com)
Grinev Vasily V., Nazarov Petr V., Klimov Eugene A.. Power-law Behavior of the Alternative Splicing of Exons in Human Transcriptome. (who.int)
Predictors of the combinatorial index values and functional outcomes of the predefined behavior of exons during splicing were also determined. (who.int)
Results: Power-law is the most plausible statistical model describing the combinatorics of exons during RNA splicing. (who.int)
Power-law behavior of exons during RNA splicing pre-determines structural diversity of transcripts, low sensitivity of splicing process to random perturbations and its high vulnerability to manipulation with highly combinative exons. (who.int)
Conclusion: Exons widely involved in alternative splicing are a part of the common power-law phenomenon in human cells. (who.int)
We identified four new splicing variants in testis that could be derived from alternative splicing of exons 8-10, 10, a part of 12-13, and 16. (elsevier.com)
The cell frequently alters the use of alternative exons in response to physiological stimuli. (umassmed.edu)
Exons that are regulated by PyrCer have in common suboptimal splice sites, are unusually short and share two 4-nt motifs, GAAR and CAAG. (umassmed.edu)
The protein binds to a conserved UGCAUG element found downstream of many alternatively spliced exons and promotes inclusion of the alternative exon in mature transcripts. (innov-research.com)
Alternative splicing involves the splicing together of other possible sets of EXONS during the processing of some, but not all, transcripts of the gene. (bvsalud.org)
Thus a particular exon may be connected to any one of several alternative exons to form a mature RNA . (bvsalud.org)
Alternatively spliced RNA transcripts that are derived from a set of exons that are located in the middle of the primary transcript (RNA PRECURSORS), between unused exons. (bvsalud.org)

Exon-exon junction spanning peptides provide direct evidence for the translation of specific splice isoforms and are critical for delineating protein isoform complexity. (nih.gov)
Our study demonstrates that detection of proteome diversity resulted from alternative splicing is limited by trypsin cleavage specificity, and that complementary digestion schemes will be essential to comprehensively analyze the translation of alternative splicing isoforms. (nih.gov)
In GBM, changes in the balance of splicing isoforms or the production of new splicing isoforms can alter the expression of the corresponding proteins and promote the generation of various malignant phenotypes. (biomedcentral.com)
We establish that human induced pluripotent stem cell (hiPSC)-derived neurons well represent the diversity of NRXN1α alternative splicing observed in the human brain, cataloguing 123 high-confidence in-frame human NRXN1α isoforms. (nature.com)
Taken together, these findings demonstrate that the mouse expresses multiple variably spliced CD44 isoforms and that expression is regulated in a tissue- and cell-type specific manner. (ox.ac.uk)
Interestingly, both phenotypes were suppressed in flies that could produce TIM proteins only from a transgene that cannot form the thermosensitive splicing isoforms. (elifesciences.org)
Indirect evidence has indicated that extensive alternative splicing of neurexin mRNAs may produce hundreds if not thousands of neurexin isoforms, but no direct evidence for such diversity has been available," they write. (pacb.com)
The alternative splice isoforms are differentially regulated in different brain regions, exhibit a diurnal cycle, and are modulated by development, neurotrophins, and neuronal activity. (pacb.com)
RNA-Seq experiments showed that amiloride not only significantly altered the level of transcript isoforms and alternative splicing events, but also deregulated the spliceosomal machinery. (nih.gov)
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. (bvsalud.org)
Several isoforms of this protein exist due to multiple alternative splicing of its MESSENGER RNA . (nih.gov)

A particularly challenging barrier to diagnosis is identifying variants that cause deleterious alternative splicing at intronic or exonic loci outside of canonical donor or acceptor splice sites. (biomedcentral.com)
The resulting model of regional splicing constraint captures differential splicing constraint across gene and exon categories, and the most constrained genic regions are enriched for pathogenic splice-altering variants. (biomedcentral.com)
ConSpliceML more accurately distinguishes deleterious and benign splicing variants than state-of-the-art splicing prediction methods, especially in "cryptic" splicing regions beyond canonical donor or acceptor splice sites. (biomedcentral.com)
Integrating a model of genetic constraint with annotations from existing alternative splicing tools allows ConSpliceML to prioritize potentially deleterious splice-altering variants in studies of rare human diseases. (biomedcentral.com)
For example, variants at canonical di-nucleotide donor or acceptor splice sites lead to mis-splicing and are frequently deleterious. (biomedcentral.com)
These estimates are based on evidence of splice-altering variants occurring beyond the exon-intron junctions. (biomedcentral.com)
Alternative splicing results in multiple transcript variants. (nih.gov)
We present here a new release of ASPicDB which now provides a unique annotation resource of human protein variants generated by alternative splicing. (unimib.it)
The expression patterns of the splicing variants in the hepatoma and colon cancer cells were different from those of the testis. (elsevier.com)
Seven haplotypes (I-VII) and four splice variants (SV154/182/183/200) with differing antiviral activities and geographic distributions have been described, but the genetic and mechanistic basis for variant expression and function remains unclear. (uthscsa.edu)
We show that SV200 is at least fourfold more HIV-1 restrictive than other A3H splice variants. (uthscsa.edu)
Thus, earlier estimates of 2,000-3,000 neurexin variants created by alternative splicing may have been an underestimate, because our present study arrived at the same numbers by analyzing only one brain region and one developmental stage. (pacb.com)
We further investigated the functionality of this region using RNA-electrophoretic mobility shift assays to show differential RNA-protein complex formation at the H1 and H2 sequence variants of SNP rs17651213 and rs1800547 and subsequently identified candidate trans-acting splicing factors interacting with these functional SNPs sequences by RNA-protein pull-down experiment and mass spectrometry. (ox.ac.uk)
CONCLUSIONS: We identified common splice factors hnRNP F and hnRNP Q regulating the haplotype-specific splicing of MAPT exon 3 through intronic variants rs1800547 and rs17651213. (ox.ac.uk)

Both baseline and drug-induced changes in AS events (ASEs) were measured using a multivariate analysis of transcript splicing (rMATS). (aacrjournals.org)
Sequence analysis revealed that the size difference in these transcripts was due to deletion of the 58 bp sequence encoded by exon II, suggesting that the smaller transcript results from an alternative splicing of the exon II sequence during processing of the β-pol precursor RNA. (utmb.edu)
The retrieval can be carried out at gene, transcript, exon, protein or splice site level allowing the selection of data sets fulfilling one or more features settled by the user. (unimib.it)
Multiple fibronectin mRNAs arise by alternative splicing of the primary transcript of a single gene. (princeton.edu)
Read lengths of up to 30 kb enabled us to identify all of the splice combinations within a single transcript," they report. (pacb.com)
The team was able to map out the full transcript landscape for a neurexin gene, showing alternative splicing at all six canonical sites as well as at several noncanonical sites. (pacb.com)

Alternative splicing (AS), one of the main post-transcriptional biological regulation mechanisms, plays a key role in the progression of glioblastoma (GBM). (biomedcentral.com)
This study is the first comprehensive view of cancer-specific circRNA alternative splicing, which could contribute significantly to regulation and functional research of circRNAs in cancers. (biomedcentral.com)
High-Resolution Expression Map of the Arabidopsis Root Reveals Alternative Splicing and lincRNA Regulation. (duke.edu)
CD44 isoform expression mediated by alternative splicing: tissue-specific regulation in mice. (ox.ac.uk)
Multiple roles of TDP-43 in gene expression, splicing regulation, and human disease. (medlineplus.gov)
Finally, gene knockdown of candidate splice factors identified by mass spectrometry demonstrate a role for hnRNP F and hnRNP Q in the haplotype-specific regulation of exon 3 inclusion. (ox.ac.uk)

In addition to these four one-domain A3 proteins, a fifth A3, designated A3CH, is expressed by read-through alternative splicing. (uni-frankfurt.de)
Splicing factors are RNA-binding proteins that regulate splicing, and manipulating splicing-factor levels could lead to therapeutic approaches for diseases with splicing-factor defects, says Anczuków. (jax.org)
A family of splicing factors known as serine/arginine-rich (SR) proteins have been implicated in a wide range of human pathologies, she notes. (jax.org)
A rational nomenclature for serine/arginine-rich protein splicing factors (SR proteins). (nih.gov)
However, the proportion of alternative transcripts and proteins actually endowed with functional activity is currently highly debated. (unimib.it)
One mechanism for establishing tissue-specific alternative splicing is by modulation of the expression levels and/or intrinsic functions of "general" RNA binding proteins (RBPs) [ 8 - 10 ]. (biomedcentral.com)
In addition, another mechanism of tissue-specific alternative splicing is mediated by "tissue-specific RBPs", which accounts for the restricted expression of many RNA binding proteins to distinct tissues or developmental stages. (biomedcentral.com)
Alternative splicing is a cellular mechanism that allows cells to produce many different proteins from a single gene. (besthealtharticle.com)
Alternative splicing allows the cell to make different proteins by combining the 'beads' in different ways. (besthealtharticle.com)
The researchers and other groups previously determined that alternative splicing regulators Rbfox1 and Rbfox2 were required for muscle development and function, but Cooper's group hypothesized that the two proteins worked together, and their combined role in adult muscle had not been studied before. (besthealtharticle.com)
We employed a computational strategy to prioritize pathogenic splicing events in human islets treated with IL-1β + IFN-γ as an ex vivo model of T1D and coupled this analysis with a k-mer based approach to predict RNA binding proteins involved in AS. (figshare.com)
We found that PyrCer binds to the PP1 catalytic subunit and inhibits the dephosphorylation of several splicing regulatory proteins containing the evolutionarily conserved RVxF PP1-binding motif (including PSF/SFPQ, Tra2-beta1 and SF2/ASF). (umassmed.edu)
Grb3-3 is an isoform of Grb2, thought to arise by alternative splicing, that lacks a functional SH2 domain but retains functional SH3 domains, which allow interaction with other proteins through binding to prolinerich sequences. (drugbank.com)

Splice sites GT-AG and CT-AC are required to support back-splicing and alternative splicing junctions. (biomedcentral.com)
It provides routines for identification, characterization and visualization of novel and existing (annotated) splice junctions from RNA-seq data. (metacpan.org)
Identification of novel splice junctions is based on intersecting potentially novel splice junctions from RNA-seq data with annotated splice junctions. (metacpan.org)
containing all its splice junctions. (metacpan.org)
is 1, canonical splice junctions are reported in the 'name' field of the output BED6 file. (metacpan.org)
Extracts splice junctions from mapped RNA-seq data. (metacpan.org)
The fifth element indicates the splice junction type: A capital 'N' determines a normal splice junction, whereas 'C' indicates circular and 'T' indicates trans-splice junctions, respectively. (metacpan.org)
Only normal splice junctions ('N') are considered, the rest is skipped. (metacpan.org)
Produce BED12 output for splice junctions found in RNA-seq data. (metacpan.org)
is 1, circular splice junctions are reported (if present in the input), else normal splice junctions are processed. (metacpan.org)
Intersects all splice junctions identified in an RNA-seq experiment with annotated splice junctions. (metacpan.org)
Identifies and characterizes novel and existing splice junctions. (metacpan.org)
All of the splicing junctions followed the conserved GT/AG rule. (elsevier.com)

The most important of these features are the abundance of exon in transcripts, the strength of splice sites, the rank of exon in transcripts and the type of exon. (who.int)
This is to prevent the tool from intersecting each splice site found in the mapped RNA-seq data with all annotated transcripts. (metacpan.org)
The relatively large size of α-neurexin transcripts (~4-5 kb) has made it difficult to obtain information about their full-length sequence, and hence about the use of alternative splice sites within single transcripts. (pacb.com)
Alternative spliced transcripts of mdig were detected in some lung cancer cell lines. (cdc.gov)

Next I will outline the way in which we use such data in our attempts to identify exon-tumor combinations exhibiting splicing patterns different from the majority. (cam.ac.uk)
Then I will briefly discuss some of the additional issues which arise when we seek to enumerate such alternative splicing patterns on a genome-wide scale. (cam.ac.uk)
In this way, we determined that 29 of 35 CRC cell lines had altered splice patterns, indicating the alternative splicing may be related to colorectal cancer. (colorado.edu)
This suggests that genome-wide alternative splicing patterns are regulated by a combination of tissue-specific cis -acting elements and "general elements" whose functional activities are important but differ across multiple tissues. (biomedcentral.com)
Evaluation of global splicing patterns using statistical approaches has the potential to reveal how combinations of cis -acting RNA elements (CAEs) contribute to tissue-specific patterns of alternative splicing. (biomedcentral.com)

Comparisons across cell types revealed that alternative splicing tends to remove parts of coding regions from a longer, major isoform, providing evidence for a progressive mechanism of splicing. (duke.edu)
Here, we analyzed a previously uncharacterized, alternative splice variant (isoform 2) of human αA-crystallin with an exchanged N-terminal sequence. (cipsm.de)
Being able to directly assess alternative splicing not only provided evidence for suspected isoform diversity, but also revealed "that neurexins are likely even more polymorphic than previously thought," the team reports. (pacb.com)
The longest gene product (isoform 1) enhances cell survival by inhibiting apoptosis while the alternatively spliced shorter gene products (isoform 2 and isoform 3) promote apoptosis and are death-inducing. (prosci-inc.com)

Alternative splicing dramatically increases transcriptome complexity but its contribution to proteome diversity remains controversial. (nih.gov)
Alternative splicing is emerging as a major mechanism for the expansion of the transcriptome and proteome diversity, particularly in human and other vertebrates. (unimib.it)
Bao H, Li E, Mansfield SD, Cronk QC, El-Kassaby YA, Douglas CJ (2013) The developing xylem transcriptome and genome-wide analysis of alternative splicing in Populus trichocarpa (black cottonwood) populations. (wikidot.com)

The advent of genome-wide splicing-sensitive microarrays provides a new perspective to address issues of combinatorial control of alternative splicing. (biomedcentral.com)

We have investigated the role of the alternative-splicing factor Sfrs1, an arginine/serine-rich (SR)protein family member, during mouse retinal development. (biologists.com)
Serine and Arginine Rich Splicing Factor 2 was implicated in 37.2% of potentially pathogenic events, including Exon5 exclusion in HLA-DMB. (figshare.com)

Alternative splicing (AS) is a co-transcriptional regulatory mechanism of plants in response to environmental stress. (bvsalud.org)

About one third of predicted CAEs can be mapped to the known RBP (RNA binding protein) binding sites or match with other predicted exonic splicing regulator databases. (biomedcentral.com)
A noticeable exception is that many exonic elements are found to regulate the alternative splicing between cerebellum and testes. (biomedcentral.com)

An AS correlation network, including 54 AS events and 94 splicing factors, was constructed, and further functional enrichment was performed. (biomedcentral.com)
Although a number of circRNAs were functionally characterized in human diseases and cancers [ 5 ], the internal structure of circRNA remains ambiguous due to potential alternative splicing, which leads to disadvantages in functional research of circRNAs. (biomedcentral.com)
We carried out a systematic analysis to characterize the potential functional consequences of alternative splicing changes in thousands of tumor samples. (hclimente.eu)
We propose that a subset of the alternative splicing changes observed in tumors may represent independent oncogenic processes that could be relevant to explain the functional transformations in cancer, and some of them could potentially be considered alternative splicing drivers (AS drivers). (hclimente.eu)

In addition, disruption of the splicing machinery in immunofluorescence studies was associated with the inhibition of myeloma cell viability after amiloride exposure. (nih.gov)

Among the 43 hits we identified was the alternative splicing regulator P-element somatic inhibitor (PSI). (elifesciences.org)
This gene encodes an RNA binding protein that is thought to be a key regulator of alternative exon splicing in the nervous system and other cell types. (innov-research.com)

Here, we proposed a de novo algorithm, CircSplice, that could identify internal alternative splicing in circRNA and compare differential circRNA splicing events between different conditions ( http://gb.whu.edu.cn/CircSplice or https://github.com/GeneFeng/CircSplice ). (biomedcentral.com)

We also established an approach largely based on the AS factor-AS events associations and identified LSM7, an alternative splicing factor, may be responsible for the major altered events. (ejbiotechnology.info)
Five-year, $2.1 million federal grant to Olga Anczuków of JAX will reveal role of splicing-factor defects in cardiac or neurological disorders, cancer and more. (jax.org)
is uncovering how splicing factors are regulated, with the goal of developing molecules to correct splicing-factor defects. (jax.org)
Characterization of SRp46, a novel human SR splicing factor encoded by a PR264/SC35 retropseudogene. (nih.gov)
The product Assay kit for Mouse Alternative Splicing Factor (ELISA) is intended to be used for research purposes only. (rnagrade.com)
The product Assay kit for Mouse Alternative Splicing Factor (ELISA) should be kept between two and eight degrees Celsius to ensure the retention of the stability and reactivity of the reagents included in the kit. (rnagrade.com)

This grant leverages our lab's expertise in developing tools and models to study splicing dysregulation in diseases," she says. (jax.org)
Loss of nuclear TDP-43 in amyotrophic lateral sclerosis (ALS) causes altered expression of splicing machinery and widespread dysregulation of RNA splicing in motor neurones. (medlineplus.gov)

ratschlab/spladder: Tool for the detection and quantification of alternative splicing events from RNA-Seq data. (github.com)

Therefore, we conclude that PSI regulates the period of Drosophila circadian rhythms and circadian behavior phase during temperature cycling through its modulation of the tim splicing pattern. (elifesciences.org)

Analysis of alternative splicing with microarrays: successes and challenges. (ucla.edu)

0.05) were identified from 19,722 alternatively spliced events. (mendeley.com)
Briefly, the software takes a given annotation and RNA-Seq read alignments in standardized formats, transforms the annotation into a splicing graph representation, augments the splicing graph with additional information extracted from the read data, extracts alternative splicing events from the graph and quantifies the events based on the alignment data. (github.com)
Then, splicing correlation network was constructed based on these AS events and associated splicing factors. (biomedcentral.com)
By applying CircSplice in clear cell renal cell carcinoma and bladder cancer, we detected 4498 and 2977 circRNA alternative splicing (circ-AS) events in the two datasets respectively and confirmed the expression of circ-AS events by RT-PCR. (biomedcentral.com)
To explore the potential variable internal structures in circRNA, we developed a de novo algorithm named CircSplice, which can identify alternative splicing events in circRNA, also called circ-AS. (biomedcentral.com)
CircSplice is a Perl script that detects potential circRNA first by back-splicing events. (biomedcentral.com)
Then, alternative splicing events within back-splicing reads and paired-end reads are identified. (biomedcentral.com)
Four circ-AS events were identified in CircSplice: skipping exon (SE), retained intron (RI), alternative 5′ splice site (A5SS) and alternative 3′ splice site (A3SS). (biomedcentral.com)
The team used Single Molecule, Real-Time (SMRT®) Sequencing to analyze full-length mRNAs from different members of the neurexin gene family and used that information to examine alternative splicing events. (pacb.com)
and the finding that splicing events seem to occur independently of one another. (pacb.com)
PlaASDB: a comprehensive database of plant alternative splicing events in response to stress. (bvsalud.org)

In this study, we present a model-based computational approach to identify potential cis -acting RNA elements by considering the exon splicing variation as the combinatorial effects of multiple cis -acting regulators. (biomedcentral.com)
These types of analytical tools are important for elucidating the combinatorial code governing splice site selection. (biomedcentral.com)

The relative lack of significant sequence similarity makes splicing a very error-prone reaction. (blogspot.com)
Note that the sequence of available ORFs provided by InvivoGen can differ from a given reference Genbank record due to genetic variations and/or alternative splicing. (invivogen.com)

The results indicate that the Rbfox splicing regulators, which are highly conserved from the worm C. elegans to humans, are essential for maintaining skeletal muscle mass in adult mice. (besthealtharticle.com)

Hypoxia plays an important role in regulating the 11 cancer hallmarks, including metabolic reprogramming, genomic instability, alternative splicing, etc. (frontiersin.org)
whose genomic location spans the query splice junction. (metacpan.org)

Perturbed splicing of the AR-V7 variant in treatment-resistant prostate cancer and MDM2 in p53 wild-type cancers were prominent examples. (aacrjournals.org)
Several existing tools predict the likelihood that a genetic variant causes alternative splicing. (biomedcentral.com)
We sought to extend such methods by developing a new metric that aids in discerning whether a genetic variant leads to deleterious alternative splicing. (biomedcentral.com)

However, it is largely unknown at the alternative splicing level which has been found to play important roles in the tumor-immune microenvironment. (ejbiotechnology.info)
Alternative splicing changes are frequently observed in cancer and are starting to be recognized as important signatures for tumor progression and therapy. (hclimente.eu)

We describe analyses of the contribution of this alternative splicing to fibronectin subunit heterogeneity in three different cell types using antisera directed against specific segments of fibronectin. (princeton.edu)
One region of alternative splicing accounts for differences in subunit size, while a second contributes to differences between the fibronectins present in blood plasma and in fibronectin cells. (princeton.edu)

Overall, our results demonstrate the antimyeloma activity of amiloride and provide a mechanistic rationale for its use as an alternative treatment option for relapsed multiple myeloma patients, especially those with 17p deletion or TP53 mutations that are resistant to current therapies. (nih.gov)

To study the impact of enzyme selection on splice junction detectability, we performed in-silico digestion of the human proteome using six proteases. (nih.gov)
Each splice junction is represented as two bed lines in the output BED6. (metacpan.org)
The fourth column in this BED file (correponding to the 'name' field according to the BED specification ) should be a colon-separated string of six elements, where the first element should be 'splits' and the second element is assumed to hold the number of reads supporting this splice junction. (metacpan.org)
BED6 files containing splice junction information from other short read mappers or third-party sources will be processed if they are formatted as described above. (metacpan.org)

This analysis revealed that a subset of alternative splicing changes affect protein domain families that are frequently mutated in tumors and potentially disrupt protein-protein interactions in cancerrelated pathways. (hclimente.eu)

Our results highlight the requirement of Sfrs1-mediated alternative splicing for the survival of retinal neurons, with sensitivity defined by the window of time in which the neuron was generated. (biologists.com)

Now, we're not talking here about so-called alternatives that are really just genetics in disguise. (nationalgeographic.com)

A wide variety of human diseases may result from defects in splicing factors, which control the version of a given gene that is expressed. (jax.org)
Single-molecule RNA FISH confirmed increased HLA-DMB splicing in pancreatic sections from human donors with established T1D and autoantibody positivity. (figshare.com)

Here we report a computational method to mechanistically identify cis -acting RNA elements that contribute to the tissue-specific alternative splicing pattern. (biomedcentral.com)
Despite an increased focus on the factors regulating tissue-specific alternative splicing, these mechanisms still remain largely unclear. (biomedcentral.com)

Anatomy15

Organisms17

Diseases6

Chemicals and Drugs62

Analytical, Diagnostic and Therapeutic Techniques and Equipment64

Psychiatry and Psychology4

Phenomena and Processes80

Disciplines and Occupations5

Anthropology, Education, Sociology and Social Phenomena1

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Geographicals1

Characterization of an amphioxus paired box gene, AmphiPax2/5/8: developmental expression patterns in optic support cells, nephridium, thyroid-like structures and pharyngeal gill slits, but not in the midbrain-hindbrain boundary region. (1/9069)

The role of gene splicing, gene amplification and regulation in mosquito insecticide resistance. (2/9069)

Expression of the naturally occurring truncated trkB neurotrophin receptor induces outgrowth of filopodia and processes in neuroblastoma cells. (3/9069)

Differential stability of the DNA-activated protein kinase catalytic subunit mRNA in human glioma cells. (4/9069)

Selection and characterization of pre-mRNA splicing enhancers: identification of novel SR protein-specific enhancer sequences. (5/9069)

Alterations in the conserved SL1 trans-spliced leader of Caenorhabditis elegans demonstrate flexibility in length and sequence requirements in vivo. (6/9069)

Mammalian staufen is a double-stranded-RNA- and tubulin-binding protein which localizes to the rough endoplasmic reticulum. (7/9069)

Expression of novel alternatively spliced isoforms of the oct-1 transcription factor. (8/9069)

No images available that match "alternative splicing"

Alternative Splicing

Complement Pathway, Alternative

Animal Testing Alternatives

Exons

Molecular Sequence Data

Complementary Therapies

Base Sequence

Protein Isoforms

Amino Acid Sequence

RNA, Messenger

RNA Splice Sites

RNA Splicing

Introns

RNA Precursors

Complement Factor B

Treatment Outcome

Complement Activation

Cloning, Molecular

Transcription, Genetic

Mutation

Time Factors

RNA-Binding Proteins

Cell Line

Polymerase Chain Reaction

DNA, Complementary

Complement C3

Models, Genetic

Sequence Alignment

Models, Biological

Reproducibility of Results

Polyadenylation

Algorithms

Gene Expression Regulation

Reverse Transcriptase Polymerase Chain Reaction

Sequence Analysis, DNA

Sensitivity and Specificity

Sequence Homology, Amino Acid

Complement C3 Convertase, Alternative Pathway

DNA Primers

DNA

Complement Pathway, Classical

Promoter Regions, Genetic

Oxidoreductases

Protein Binding

Evolution, Molecular

Properdin

Organ Specificity

RNA Isoforms

Complement Factor D

Phylogeny

Gene Expression Profiling

Cells, Cultured

Binding Sites

Sequence Homology, Nucleic Acid

Protein Structure, Tertiary

Complement C3-C5 Convertases

Computer Simulation

Computational Biology

HeLa Cells

Transfection

Nuclear Proteins

Phenotype

Gene Expression

Choice Behavior

Genetic Variation

Recombinant Proteins

Models, Molecular

Expressed Sequence Tags

Species Specificity

Kinetics

Models, Statistical

Transcription Factors

Signal Transduction

Complement C3b

Conserved Sequence

Bacterial Proteins

RNA

Cost-Benefit Analysis

Proteins

Escherichia coli