Rna splicing. Medical search

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)

Small double-stranded, non-protein coding RNAs (21-31 nucleotides) involved in GENE SILENCING functions, especially RNA INTERFERENCE (RNAi). Endogenously, siRNAs are generated from dsRNAs (RNA, DOUBLE-STRANDED) by the same ribonuclease, Dicer, that generates miRNAs (MICRORNAS). The perfect match of the siRNAs' antisense strand to their target RNAs mediates RNAi by siRNA-guided RNA cleavage. siRNAs fall into different classes including trans-acting siRNA (tasiRNA), repeat-associated RNA (rasiRNA), small-scan RNA (scnRNA), and Piwi protein-interacting RNA (piRNA) and have different specific gene silencing functions.

Ribonucleic acid that makes up the genetic material of viruses.

A process that changes the nucleotide sequence of mRNA from that of the DNA template encoding it. Some major classes of RNA editing are as follows: 1, the conversion of cytosine to uracil in mRNA; 2, the addition of variable number of guanines at pre-determined sites; and 3, the addition and deletion of uracils, templated by guide-RNAs (RNA, GUIDE).

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

The most abundant form of RNA. Together with proteins, it forms the ribosomes, playing a structural role and also a role in ribosomal binding of mRNA and tRNAs. Individual chains are conventionally designated by their sedimentation coefficients. In eukaryotes, four large chains exist, synthesized in the nucleolus and constituting about 50% of the ribosome. (Dorland, 28th ed)

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

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

Viruses whose genetic material is RNA.

A gene silencing phenomenon whereby specific dsRNAs (RNA, DOUBLE-STRANDED) trigger the degradation of homologous mRNA (RNA, MESSENGER). The specific dsRNAs are processed into SMALL INTERFERING RNA (siRNA) which serves as a guide for cleavage of the homologous mRNA in the RNA-INDUCED SILENCING COMPLEX. DNA METHYLATION may also be triggered during this process.

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.

RNA consisting of two strands as opposed to the more prevalent single-stranded RNA. Most of the double-stranded segments are formed from transcription of DNA by intramolecular base-pairing of inverted complementary sequences separated by a single-stranded loop. Some double-stranded segments of RNA are normal in all organisms.

RNA that has catalytic activity. The catalytic RNA sequence folds to form a complex surface that can function as an enzyme in reactions with itself and other molecules. It may function even in the absence of protein. There are numerous examples of RNA species that are acted upon by catalytic RNA, however the scope of this enzyme class is not limited to a particular type of substrate.

The processes of RNA tertiary structure formation.

A DNA-dependent RNA polymerase present in bacterial, plant, and animal cells. It functions in the nucleoplasmic structure and transcribes DNA into RNA. It has different requirements for cations and salt than RNA polymerase I and is strongly inhibited by alpha-amanitin. EC 2.7.7.6.

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

The extent to which an RNA molecule retains its structural integrity and resists degradation by RNASE, and base-catalyzed HYDROLYSIS, under changing in vivo or in vitro conditions.

A family of proteins that promote unwinding of RNA during splicing and translation.

RNA molecules which hybridize to complementary sequences in either RNA or DNA altering the function of the latter. Endogenous antisense RNAs function as regulators of gene expression by a variety of mechanisms. Synthetic antisense RNAs are used to effect the functioning of specific genes for investigative or therapeutic purposes.

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 small RNA molecules, 73-80 nucleotides long, that function during translation (TRANSLATION, GENETIC) to align AMINO ACIDS at the RIBOSOMES in a sequence determined by the mRNA (RNA, MESSENGER). There are about 30 different transfer RNAs. Each recognizes a specific CODON set on the mRNA through its own ANTICODON and as aminoacyl tRNAs (RNA, TRANSFER, AMINO ACYL), each carries a specific amino acid to the ribosome to add to the elongating peptide chains.

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

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.

RNA which does not code for protein but has some enzymatic, structural or regulatory function. Although ribosomal RNA (RNA, RIBOSOMAL) and transfer RNA (RNA, TRANSFER) are also untranslated RNAs they are not included in this scope.

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

Nucleic acid structures found on the 5' end of eukaryotic cellular and viral messenger RNA and some heterogeneous nuclear RNAs. These structures, which are positively charged, protect the above specified RNAs at their termini against attack by phosphatases and other nucleases and promote mRNA function at the level of initiation of translation. Analogs of the RNA caps (RNA CAP ANALOGS), which lack the positive charge, inhibit the initiation of protein synthesis.

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

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

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

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

RNA present in neoplastic tissue.

An enzyme that catalyzes the conversion of linear RNA to a circular form by the transfer of the 5'-phosphate to the 3'-hydroxyl terminus. It also catalyzes the covalent joining of two polyribonucleotides in phosphodiester linkage. EC 6.5.1.3.

A large family of RNA helicases that share a common protein motif with the single letter amino acid sequence D-E-A-D (Asp-Glu-Ala-Asp). In addition to RNA helicase activity, members of the DEAD-box family participate in other aspects of RNA metabolism and regulation of RNA function.

A DNA-dependent RNA polymerase present in bacterial, plant, and animal cells. It functions in the nucleoplasmic structure where it transcribes DNA into RNA. It has specific requirements for cations and salt and has shown an intermediate sensitivity to alpha-amanitin in comparison to RNA polymerase I and II. EC 2.7.7.6.

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.

A DNA-dependent RNA polymerase present in bacterial, plant, and animal cells. The enzyme functions in the nucleolar structure and transcribes DNA into RNA. It has different requirements for cations and salts than RNA polymerase II and III and is not inhibited by alpha-amanitin. EC 2.7.7.6.

RNA molecules found in the nucleus either associated with chromosomes or in the nucleoplasm.

Small kinetoplastid mitochondrial RNA that plays a major role in RNA EDITING. These molecules form perfect hybrids with edited mRNA sequences and possess nucleotide sequences at their 5'-ends that are complementary to the sequences of the mRNA's immediately downstream of the pre-edited regions.

Constituent of the 60S subunit of eukaryotic ribosomes. 28S rRNA is involved in the initiation of polypeptide synthesis in eukaryotes.

Constituent of the 40S subunit of eukaryotic ribosomes. 18S rRNA is involved in the initiation of polypeptide synthesis in eukaryotes.

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

Constituent of 50S subunit of prokaryotic ribosomes containing about 3200 nucleotides. 23S rRNA is involved in the initiation of polypeptide synthesis.

The process of moving specific RNA molecules from one cellular compartment or region to another by various sorting and transport mechanisms.

The small RNAs which provide spliced leader sequences, SL1, SL2, SL3, SL4 and SL5 (short sequences which are joined to the 5' ends of pre-mRNAs by TRANS-SPLICING). They are found primarily in primitive eukaryotes (protozoans and nematodes).

Small, linear single-stranded RNA molecules functionally acting as molecular parasites of certain RNA plant viruses. Satellite RNAs exhibit four characteristic traits: (1) they require helper viruses to replicate; (2) they are unnecessary for the replication of helper viruses; (3) they are encapsidated in the coat protein of the helper virus; (4) they have no extensive sequence homology to the helper virus. Thus they differ from SATELLITE VIRUSES which encode their own coat protein, and from the genomic RNA; (=RNA, VIRAL); of satellite viruses. (From Maramorosch, Viroids and Satellites, 1991, p143)

Constituent of 30S subunit prokaryotic ribosomes containing 1600 nucleotides and 21 proteins. 16S rRNA is involved in initiation of polypeptide synthesis.

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.

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

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

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

Established cell cultures that have the potential to propagate indefinitely.

The process of intracellular viral multiplication, consisting of the synthesis of PROTEINS; NUCLEIC ACIDS; and sometimes LIPIDS, and their assembly into a new infectious particle.

A 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 reaction that severs one of the sugar-phosphate linkages of the phosphodiester backbone of RNA. It is catalyzed enzymatically, chemically, or by radiation. Cleavage may be exonucleolytic, or endonucleolytic.

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.

A group of ribonucleotides (up to 12) in which the phosphate residues of each ribonucleotide act as bridges in forming diester linkages between the ribose moieties.

Nuclear nonribosomal RNA larger than about 1000 nucleotides, the mass of which is rapidly synthesized and degraded within the cell nucleus. Some heterogeneous nuclear RNA may be a precursor to mRNA. However, the great bulk of total hnRNA hybridizes with nuclear DNA rather than with mRNA.

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

Small RNAs found in the cytoplasm usually complexed with proteins in scRNPs (RIBONUCLEOPROTEINS, SMALL CYTOPLASMIC).

The steps that generate the 3' ends of mature RNA molecules. For most mRNAs (RNA, MESSENGER), 3' end processing referred to as POLYADENYLATION includes the addition of POLY A.

Macromolecular molds for the synthesis of complementary macromolecules, as in DNA REPLICATION; GENETIC TRANSCRIPTION of DNA to RNA, and GENETIC TRANSLATION of RNA into POLYPEPTIDES.

Short RNA, about 200 base pairs in length or shorter, that does not code for protein.

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.

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

Enzymes that catalyze the hydrolysis of ester bonds within RNA. EC 3.1.-.

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.

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

Constituent of the 60S subunit of eukaryotic ribosomes. 5.8S rRNA is involved in the initiation of polypeptide synthesis in eukaryotes.

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).

A class of untranslated RNA molecules that are typically greater than 200 nucleotides in length and do not code for proteins. Members of this class have been found to play roles in transcriptional regulation, post-transcriptional processing, CHROMATIN REMODELING, and in the epigenetic control of chromatin.

Small nuclear RNAs that are involved in the processing of pre-ribosomal RNA in the nucleolus. Box C/D containing snoRNAs (U14, U15, U16, U20, U21 and U24-U63) direct site-specific methylation of various ribose moieties. Box H/ACA containing snoRNAs (E2, E3, U19, U23, and U64-U72) direct the conversion of specific uridines to pseudouridine. Site-specific cleavages resulting in the mature ribosomal RNAs are directed by snoRNAs U3, U8, U14, U22 and the snoRNA components of RNase MRP and RNase P.

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

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.

Synthetic transcripts of a specific DNA molecule or fragment, made by an in vitro transcription system. This cRNA can be labeled with radioactive uracil and then used as a probe. (King & Stansfield, A Dictionary of Genetics, 4th ed)

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

A family of enzymes that catalyze the endonucleolytic cleavage of RNA. It includes EC 3.1.26.-, EC 3.1.27.-, EC 3.1.30.-, and EC 3.1.31.-.

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)

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

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

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

The rate dynamics in chemical or physical systems.

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

Pairing of purine and pyrimidine bases by HYDROGEN BONDING in double-stranded DNA or RNA.

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

Viruses parasitic on plants higher than bacteria.

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

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

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

A transfer RNA which is specific for carrying phenylalanine to sites on the ribosomes in preparation for protein synthesis.

A transfer RNA which is specific for carrying lysine to sites on the ribosomes in preparation for protein synthesis.

Multicomponent ribonucleoprotein structures found in the CYTOPLASM of all cells, and in MITOCHONDRIA, and PLASTIDS. They function in PROTEIN BIOSYNTHESIS via GENETIC TRANSLATION.

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.

Deoxyribonucleic acid that makes up the genetic material of viruses.

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.

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

Interruption or suppression of the expression of a gene at transcriptional or translational levels.

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.

A transfer RNA which is specific for carrying tyrosine to sites on the ribosomes in preparation for protein synthesis.

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

Cyclic peptides extracted from carpophores of various mushroom species. They are potent inhibitors of RNA polymerases in most eukaryotic species, blocking the production of mRNA and protein synthesis. These peptides are important in the study of transcription. Alpha-amanitin is the main toxin from the species Amanitia phalloides, poisonous if ingested by humans or animals.

The functional hereditary units of VIRUSES.

Disruption of the secondary structure of nucleic acids by heat, extreme pH or chemical treatment. Double strand DNA is "melted" by dissociation of the non-covalent hydrogen bonds and hydrophobic interactions. Denatured DNA appears to be a single-stranded flexible structure. The effects of denaturation on RNA are similar though less pronounced and largely reversible.

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.

An enzyme catalyzing the endonucleolytic cleavage of RNA at the 3'-position of a guanylate residue. EC 3.1.27.3.

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

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

Within most types of eukaryotic CELL NUCLEUS, a distinct region, not delimited by a membrane, in which some species of rRNA (RNA, RIBOSOMAL) are synthesized and assembled into ribonucleoprotein subunits of ribosomes. In the nucleolus rRNA is transcribed from a nucleolar organizer, i.e., a group of tandemly repeated chromosomal genes which encode rRNA and which are transcribed by RNA polymerase I. (Singleton & Sainsbury, Dictionary of Microbiology & Molecular Biology, 2d ed)

The type species of LENTIVIRUS and the etiologic agent of AIDS. It is characterized by its cytopathic effect and affinity for the T4-lymphocyte.

A fractionated cell extract that maintains a biological function. A subcellular fraction isolated by ultracentrifugation or other separation techniques must first be isolated so that a process can be studied free from all of the complex side reactions that occur in a cell. The cell-free system is therefore widely used in cell biology. (From Alberts et al., Molecular Biology of the Cell, 2d ed, p166)

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.

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.

Any of the processes by which cytoplasmic factors influence the differential control of gene action in viruses.

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.

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 encoded by a VIRAL GENOME that are produced in the organisms they infect, but not packaged into the VIRUS PARTICLES. Some of these proteins may play roles within the infected cell during VIRUS REPLICATION or act in regulation of virus replication or VIRUS ASSEMBLY.

Intermediates in protein biosynthesis. The compounds are formed from amino acids, ATP and transfer RNA, a reaction catalyzed by aminoacyl tRNA synthetase. They are key compounds in the genetic translation process.

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

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.

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.

A transfer RNA which is specific for carrying alanine to sites on the ribosomes in preparation for protein synthesis.

A species of ENTEROVIRUS which is the causal agent of POLIOMYELITIS in humans. Three serotypes (strains) exist. Transmission is by the fecal-oral route, pharyngeal secretions, or mechanical vector (flies). Vaccines with both inactivated and live attenuated virus have proven effective in immunizing against the infection.

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.

A plant genus of the family SOLANACEAE. Members contain NICOTINE and other biologically active chemicals; its dried leaves are used for SMOKING.

An RNA-containing enzyme that plays an essential role in tRNA processing by catalyzing the endonucleolytic cleavage of TRANSFER RNA precursors. It removes the extra 5'-nucleotides from tRNA precursors to generate mature tRNA molecules.

Separation of particles according to density by employing a gradient of varying densities. At equilibrium each particle settles in the gradient at a point equal to its density. (McGraw-Hill Dictionary of Scientific and Technical Terms, 4th ed)

The part of a cell that contains the CYTOSOL and small structures excluding the CELL NUCLEUS; MITOCHONDRIA; and large VACUOLES. (Glick, Glossary of Biochemistry and Molecular Biology, 1990)

The monomeric units from which DNA or RNA polymers are constructed. They consist of a purine or pyrimidine base, a pentose sugar, and a phosphate group. (From King & Stansfield, A Dictionary of Genetics, 4th ed)

Viruses which produce a mottled appearance of the leaves of plants.

An enzyme that synthesizes DNA on an RNA template. It is encoded by the pol gene of retroviruses and by certain retrovirus-like elements. EC 2.7.7.49.

A compound composed of a two CYCLIC PEPTIDES attached to a phenoxazine that is derived from STREPTOMYCES parvullus. It binds to DNA and inhibits RNA synthesis (transcription), with chain elongation more sensitive than initiation, termination, or release. As a result of impaired mRNA production, protein synthesis also declines after dactinomycin therapy. (From AMA Drug Evaluations Annual, 1993, p2015)

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

A genus of FLAVIVIRIDAE causing parenterally-transmitted HEPATITIS C which is associated with transfusions and drug abuse. Hepatitis C virus is the type species.

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

A transfer RNA which is specific for carrying aspartic acid to sites on the ribosomes in preparation for protein synthesis.

A transfer RNA which is specific for carrying methionine to sites on the ribosomes. During initiation of protein synthesis, tRNA(f)Met in prokaryotic cells and tRNA(i)Met in eukaryotic cells binds to the start codon (CODON, INITIATOR).

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

A genus of tripartite plant viruses in the family BROMOVIRIDAE. Transmission is by beetles. Brome mosaic virus is the type species.

Proteins prepared by recombinant DNA technology.

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

A ribonuclease that specifically cleaves the RNA moiety of RNA:DNA hybrids. It has been isolated from a wide variety of prokaryotic and eukaryotic organisms as well as RETROVIRUSES.

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.

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.

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

A multiribosomal structure representing a linear array of RIBOSOMES held together by messenger RNA; (RNA, MESSENGER); They represent the active complexes in cellular protein synthesis and are able to incorporate amino acids into polypeptides both in vivo and in vitro. (From Rieger et al., Glossary of Genetics: Classical and Molecular, 5th ed)

A cell line derived from cultured tumor cells.

The outer protein protective shell of a virus, which protects the viral nucleic acid.

A family of enzymes that catalyze the exonucleolytic cleavage of RNA. It includes EC 3.1.13.-, EC 3.1.14.-, EC 3.1.15.-, and EC 3.1.16.-. EC 3.1.-

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.

Proteins found in any species of bacterium.

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

A transfer RNA which is specific for carrying glycine to sites on the ribosomes in preparation for protein synthesis.

A transfer RNA which is specific for carrying histidine to sites on the ribosomes in preparation for protein synthesis.

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

A transfer RNA which is specific for carrying valine to sites on the ribosomes in preparation for protein synthesis.

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

A family of RNA viruses infecting insects and fish. There are two genera: Alphanodavirus and Betanodavirus.

Use for nucleic acid precursors in general or for which there is no specific heading.

The assembly of VIRAL STRUCTURAL PROTEINS and nucleic acid (VIRAL DNA or VIRAL RNA) to form a VIRUS PARTICLE.

Viruses which lack a complete genome so that they cannot completely replicate or cannot form a protein coat. Some are host-dependent defectives, meaning they can replicate only in cell systems which provide the particular genetic function which they lack. Others, called SATELLITE VIRUSES, are able to replicate only when their genetic defect is complemented by a helper virus.

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

A transfer RNA which is specific for carrying arginine to sites on the ribosomes in preparation for protein synthesis.

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

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

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.

Proteins obtained from ESCHERICHIA COLI.

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.

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.

The infective system of a virus, composed of the viral genome, a protein core, and a protein coat called a capsid, which may be naked or enclosed in a lipoprotein envelope called the peplos.

Highly conserved nuclear RNA-protein complexes that function in RNA processing in the nucleus, including pre-mRNA splicing and pre-mRNA 3'-end processing in the nucleoplasm, and pre-rRNA processing in the nucleolus (see RIBONUCLEOPROTEINS, SMALL NUCLEOLAR).

A defective virus, containing particles of RNA nucleoprotein in virion-like form, present in patients with acute hepatitis B and chronic hepatitis. It requires the presence of a hepadnavirus for full replication. This is the lone species in the genus Deltavirus.

Proteins found in ribosomes. They are believed to have a catalytic function in reconstituting biologically active ribosomal subunits.

A transfer RNA which is specific for carrying tryptophan to sites on the ribosomes in preparation for protein synthesis.

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.

DNA sequences recognized as signals to end GENETIC TRANSCRIPTION.

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.

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

Multicellular, eukaryotic life forms of kingdom Plantae (sensu lato), comprising the VIRIDIPLANTAE; RHODOPHYTA; and GLAUCOPHYTA; all of which acquired chloroplasts by direct endosymbiosis of CYANOBACTERIA. They are characterized by a mainly photosynthetic mode of nutrition; essentially unlimited growth at localized regions of cell divisions (MERISTEMS); cellulose within cells providing rigidity; the absence of organs of locomotion; absence of nervous and sensory systems; and an alternation of haploid and diploid generations.

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

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

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

A bacteriophage genus of the family LEVIVIRIDAE, whose viruses contain the short version of the genome and have a separate gene for cell lysis.

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 hemoflagellate subspecies of parasitic protozoa that causes nagana in domestic and game animals in Africa. It apparently does not infect humans. It is transmitted by bites of tsetse flies (Glossina).

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

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 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.

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

A genus of plant viruses that infects ANGIOSPERMS. Transmission occurs mechanically and through soil, with one species transmitted via a fungal vector. The type species is Tomato bushy stunt virus.

A purine nucleoside that has guanine linked by its N9 nitrogen to the C1 carbon of ribose. It is a component of ribonucleic acid and its nucleotides play important roles in metabolism. (From Dorland, 28th ed)

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 transfer RNA which is specific for carrying leucine to sites on the ribosomes in preparation for protein synthesis.

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

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

Addition of methyl groups. In histo-chemistry methylation is used to esterify carboxyl groups and remove sulfate groups by treating tissue sections with hot methanol in the presence of hydrochloric acid. (From Stedman, 25th ed)

JNK2 is required for efficient T-cell activation and apoptosis but not for normal lymphocyte development. (1/7106)

BACKGROUND: The Jun N-terminal kinase (JNK) signaling pathway has been implicated in cell proliferation and apoptosis, but its function seems to depend on the cell type and inducing signal. In T cells, JNK has been implicated in both antigen-induced activation and apoptosis. RESULTS: We generated mice lacking the JNK2 isozymes. The mutant mice were healthy and fertile but defective in peripheral T-cell activation induced by antibody to the CD3 component of the T-cell receptor (TCR) complex - proliferation and production of interleukin-2 (IL-2), IL-4 and interferon-gamma (IFN-gamma) were reduced. The proliferation defect was restored by exogenous IL-2. B-cell activation was normal in the absence of JNK2. Activation-induced peripheral T-cell apoptosis was comparable between mutant and wild-type mice, but immature (CD4(+) CD8(+)) thymocytes lacking JNK2 were resistant to apoptosis induced by administration of anti-CD3 antibody in vivo. The lack of JNK2 also resulted in partial resistance of thymocytes to anti-CD3 antibody in vitro, but had little or no effect on apoptosis induced by anti-Fas antibody, dexamethasone or ultraviolet-C (UVC) radiation. CONCLUSIONS: JNK2 is essential for efficient activation of peripheral T cells but not B cells. Peripheral T-cell activation is probably required indirectly for induction of thymocyte apoptosis resulting from administration of anti-CD3 antibody in vivo. JNK2 functions in a cell-type-specific and stimulus-dependent manner, being required for apoptosis of immature thymocytes induced by anti-CD3 antibody but not for apoptosis induced by anti-Fas antibody, UVC or dexamethasone. JNK2 is not required for activation-induced cell death of mature T cells. (+info)

In vivo expression of the nucleolar group I intron-encoded I-dirI homing endonuclease involves the removal of a spliceosomal intron. (2/7106)

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

The splicing factor-associated protein, p32, regulates RNA splicing by inhibiting ASF/SF2 RNA binding and phosphorylation. (3/7106)

The cellular protein p32 was isolated originally as a protein tightly associated with the essential splicing factor ASF/SF2 during its purification from HeLa cells. ASF/SF2 is a member of the SR family of splicing factors, which stimulate constitutive splicing and regulate alternative RNA splicing in a positive or negative fashion, depending on where on the pre-mRNA they bind. Here we present evidence that p32 interacts with ASF/SF2 and SRp30c, another member of the SR protein family. We further show that p32 inhibits ASF/SF2 function as both a splicing enhancer and splicing repressor protein by preventing stable ASF/SF2 interaction with RNA, but p32 does not block SRp30c function. ASF/SF2 is highly phosphorylated in vivo, a modification required for stable RNA binding and protein-protein interaction during spliceosome formation, and this phosphorylation, either through HeLa nuclear extracts or through specific SR protein kinases, is inhibited by p32. Our results suggest that p32 functions as an ASF/SF2 inhibitory factor, regulating ASF/SF2 RNA binding and phosphorylation. These findings place p32 into a new group of proteins that control RNA splicing by sequestering an essential RNA splicing factor into an inhibitory complex. (+info)

Tight binding of the 5' exon to domain I of a group II self-splicing intron requires completion of the intron active site. (4/7106)

Group II self-splicing requires the 5' exon to form base pairs with two stretches of intronic sequence (EBS1 and EBS2) which also bind the DNA target during retrotransposition of the intron. We have used dimethyl sulfate modification of bases to obtain footprints of the 5' exon on intron Pl.LSU/2 from the mitochondrion of the alga Pylaiella littoralis, as well as on truncated intron derivatives. Aside from the EBS sites, which are part of the same subdomain (ID) of ribozyme secondary structure, three distant adenines become either less or more sensitive to modification in the presence of the exon. Unexpectedly, one of these adenines in subdomain IC1 is footprinted only in the presence of the distal helix of domain V, which is involved in catalysis. While the loss of that footprint is accompanied by a 100-fold decrease in the affinity for the exon, both protection from modification and efficient binding can be restored by a separate domain V transcript, whose binding results in its own, concise footprint on domains I and III. Possible biological implications of the need for the group II active site to be complete in order to observe high-affinity binding of the 5' exon to domain I are discussed. (+info)

A premature termination codon interferes with the nuclear function of an exon splicing enhancer in an open reading frame-dependent manner. (5/7106)

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

Substrate specificities of SR proteins in constitutive splicing are determined by their RNA recognition motifs and composite pre-mRNA exonic elements. (6/7106)

We report striking differences in the substrate specificities of two human SR proteins, SF2/ASF and SC35, in constitutive splicing. beta-Globin pre-mRNA (exons 1 and 2) is spliced indiscriminately with either SR protein. Human immunodeficiency virus tat pre-mRNA (exons 2 and 3) and immunoglobulin mu-chain (IgM) pre-mRNA (exons C3 and C4) are preferentially spliced with SF2/ASF and SC35, respectively. Using in vitro splicing with mutated or chimeric derivatives of the tat and IgM pre-mRNAs, we defined specific combinations of segments in the downstream exons, which mediate either positive or negative effects to confer SR protein specificity. A series of recombinant chimeric proteins consisting of domains of SF2/ASF and SC35 in various combinations was used to localize trans-acting domains responsible for substrate specificity. The RS domains of SF2/ASF and SC35 can be exchanged without effect on substrate specificity. The RNA recognition motifs (RRMs) of SF2/ASF are active only in the context of a two-RRM structure, and RRM2 has a dominant role in substrate specificity. In contrast, the single RRM of SC35 can function alone, but its substrate specificity can be influenced by the presence of an additional RRM. The RRMs behave as modules that, when present in different combinations, can have positive, neutral, or negative effects on splicing, depending upon the specific substrate. We conclude that SR protein-specific recognition of specific positive and negative pre-mRNA exonic elements via one or more RRMs is a crucial determinant of the substrate specificity of SR proteins in constitutive splicing. (+info)

Alterations in the conserved SL1 trans-spliced leader of Caenorhabditis elegans demonstrate flexibility in length and sequence requirements in vivo. (7/7106)

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)

A novel genetic screen for snRNP assembly factors in yeast identifies a conserved protein, Sad1p, also required for pre-mRNA splicing. (8/7106)

The assembly pathway of spliceosomal snRNPs in yeast is poorly understood. We devised a screen to identify mutations blocking the assembly of newly synthesized U4 snRNA into a functional snRNP. Fifteen mutant strains failing either to accumulate the newly synthesized U4 snRNA or to assemble a U4/U6 particle were identified and categorized into 13 complementation groups. Thirteen previously identified splicing-defective prp mutants were also assayed for U4 snRNP assembly defects. Mutations in the U4/U6 snRNP components Prp3p, Prp4p, and Prp24p led to disassembly of the U4/U6 snRNP particle and degradation of the U6 snRNA, while prp17-1 and prp19-1 strains accumulated free U4 and U6 snRNA. A detailed analysis of a newly identified mutant, the sad1-1 mutant, is presented. In addition to having the snRNP assembly defect, the sad1-1 mutant is severely impaired in splicing at the restrictive temperature: the RP29 pre-mRNA strongly accumulates and splicing-dependent production of beta-galactosidase from reporter constructs is abolished, while extracts prepared from sad1-1 strains fail to splice pre-mRNA substrates in vitro. The sad1-1 mutant is the only splicing-defective mutant analyzed whose mutation preferentially affects assembly of newly synthesized U4 snRNA into the U4/U6 particle. SAD1 encodes a novel protein of 52 kDa which is essential for cell viability. Sad1p localizes to the nucleus and is not stably associated with any of the U snRNAs. Sad1p contains a putative zinc finger and is phylogenetically highly conserved, with homologues identified in human, Caenorhabditis elegans, Arabidospis, and Drosophila. (+info)

Several methods of RNA splicing occur in nature; the type of splicing depends on the structure of the spliced intron and the ... Eukaryotes splice many protein-coding messenger RNAs and some non-coding RNAs. Prokaryotes, on the other hand, splice rarely ... Eul J, Patzel V (Oct 2013). "Homologous SV40 RNA trans-splicing". RNA Biology. 10 (11): 1689-1699. doi:10.4161/rna.26707. PMID ... Trans-splicing is a form of splicing that removes introns or outrons, and joins two exons that are not within the same RNA ...

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

Total RNA is purified from the specimen of interest. Poly A messenger RNA is then purified from total RNA and subsequently ... end of the messenger RNA require the presence of a trans-spliced leader sequence. Spliced leader sequences are short sequences ... Trans-Spliced Exon Coupled RNA End Determination (TEC-RED) is a transcriptomic technique that, like SAGE, allows for the ... Huang XY, Hirsh D (November 1989). "A second trans-spliced RNA leader sequence in the nematode Caenorhabditis elegans". Proc. ...

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

RNA. 14 (5): 802-813. doi:10.1261/rna.876308. ISSN 1355-8382. PMC 2327353. PMID 18369186. (Spliceosome, RNA splicing). ... exonic splicing silencers (ESSs) present in introns: intronic splicing enhancers (ISEs), intronic splicing silencers (ISSs). ... Splicing regulatory element (SRE) are cis-acting sequences in pre-mRNA, which either enhance or silence (suppress) the splicing ... SREs recruit trans-acting splicing factors to activate or suppress the splice site recognition or spliceosome assembly. The " ...

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

... 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 differs from cis-splicing in that there is no 5' splice site on the pre-mRNA. Instead the 5' splice site is ... Alternative trans-splicing includes intragenic trans-splicing and intergenic trans-splicing. Intragenic trans-splicing involves ... Trans-splicing is a special form of RNA processing where exons from two different primary RNA transcripts are joined end to end ...

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

... , or alternative RNA splicing, or differential splicing, is an alternative splicing process during gene ... Such proteins include splicing activators that promote the usage of a particular splice site, and splicing repressors that ... The regulation and selection of splice sites are done by trans-acting splicing activator and splicing repressor proteins as ... RNA. 15 (12): 2385-97. doi:10.1261/rna.1821809. PMC 2779669. PMID 19861426. Wang Z, Burge CB (May 2008). "Splicing regulation: ...

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

AspicDB ECgene RNA splicing Kim, Namshin; Alekseyenko Alexander V; Roy Meenakshi; Lee Christopher (Jan 2007). "The ASAP II ... Alternative Splicing Annotation Project (ASAP) in computational biology was a database for alternative splicing data maintained ... RNA splicing, All stub articles, Biological database stubs). ... analysis and comparative genomics of alternative splicing in 15 ... Lee, Christopher; Atanelov, Levan; Modrek, Barmak; Xing, Yi (2003-01-01). "ASAP: the Alternative Splicing Annotation Project". ...

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

Cell biology and genomics RNA interference (RNAi) and small-RNA biology; DNA replication; RNA splicing; signal transduction; ... which revealed the RNA splicing mechanism. James D. Watson, shared a Nobel Prize with Francis Crick and Maurice Wilkins in 1962 ... genome structure; non-coding RNAs; deep sequencing; single-cell sequencing and analytics; stem cell self-renewal and ...

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

Li; Wang, J; Mor, G; Sklar, J (2008). "A neoplastic gene fusion mimics trans-splicing of RNAs in normal human cells". Science. ... Fusion transcript is a chimeric RNA encoded by a fusion gene or by two different genes by subsequent trans-splicing. Certain ...

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

See also RNA splicing. amber One of three stop codons used in the standard genetic code; in RNA, it is specified by the ... RNA-RNA, or a DNA-RNA hybrid) which are held together by hydrogen bonds between the complementary nucleobases of each strand, ... gRNA See guide RNA. guanine (G) A purine nucleobase used as one of the four standard nucleobases in both DNA and RNA molecules ... long non-coding RNA (lncRNA) A class of non-coding RNA consisting of all transcripts of more than 200 nucleotides in length ...

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

See also RNA splicing. amber One of three stop codons used in the standard genetic code; in RNA, it is specified by the ... RNA gene A gene that codes for any of the various types of non-coding RNAs (e.g. rRNAs and tRNAs). RNA interference (RNAi) RNA ... small interfering RNA (siRNA) small nuclear RNA (snRNA) small nucleolar RNA (snoRNA) small temporal RNA (stRNA) A subclass of ... snoRNA See small nucleolar RNA. snRNA See small nuclear RNA. solenoid fiber soluble RNA (sRNA) See transfer RNA. somatic cell ...

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

Alternative Splicing Annotation Project AspicDB RNA splicing Koscielny, Gautier; Le Texier, Vincent; Gopalakrishnan, Chellappa ... RNA splicing, Science and technology in Cambridgeshire, South Cambridgeshire District, All stub articles, Biological database ... "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 ...

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

Intragenomic conflict Intron Protein tag RNA splicing Bowman, EJ; Tenney, K; Bowman, BJ (Oct 1988). "Isolation of genes ... Protein Splicing, 2007 Protein splicing mechanism and intein structure Protein+Splicing at the US National Library of Medicine ... After splicing has taken place, the resulting protein contains the N-extein linked to the C-extein; this splicing product is ... with a peptide bond during protein splicing. Inteins have also been called protein introns, by analogy with (RNA) introns. The ...

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

The bZIP intron RNA motif is an RNA structure guiding splicing of a non-canonical intron from bZIP-containing genes called HAC1 ... IRE1 recognizes splice-site motifs in bZIP transcript and cleaves it. Stem-loop structures around the splice sites and IRE1- ... Hooks KB, Griffiths-Jones S (2011). "Conserved RNA structures in the non-canonical Hac1/Xbp1 intron". RNA Biol. 8 (4): 552-556 ... that brings the splice sites together (see figure). The sequence of the intron is well conserved only around the splice sites. ...

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

The RNA structure consists of two hairpins of similar length with loop regions defining the splice sites. Intron is usually 23 ... The splicing mechanism in this group was first reported in human. Hooks KB, Griffiths-Jones S (2011). "Conserved RNA structures ... doi:10.4161/rna.8.4.15396. PMC 3225973. PMID 21593604. Yoshida H, Matsui T, Yamamoto A, Okada T, Mori K (2001). "XBP1 mRNA is ... induced by ATF6 and spliced by IRE1 in response to ER stress to produce a highly active transcription factor". Cell. 107 (7): ...

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

... known as a donor splice site (or 5' splice site) and an acceptor splice site (or 3' splice site), respectively. The 5' splice ... suggesting that the circular RNA formation is generally coupled to RNA splicing. It was determined that most circular RNAs ... Trans-splicing is very common in C. elegans A splice donor site being joined to a splice acceptor site further upstream in the ... Circular RNA (or circRNA) is a type of single-stranded RNA which, unlike linear RNA, forms a covalently closed continuous loop ...

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

RNA splicing, Non-coding RNA). ... The consensus RNA structure is very similar to the animal ... Hooks KB, Griffiths-Jones S (2011). "Conserved RNA structures in the non-canonical Hac1/Xbp1 intron". RNA Biol. 8 (4): 552-556 ... The unconventional splicing in this group is performed by IRE1 in response to ER stress and it was first described in ... doi:10.4161/rna.8.4.15396. PMC 3225973. PMID 21593604. Deng, Y.; Humbert, S.; Liu, J.-X.; Srivastava, R.; Rothstein, S. J.; ...

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

"Aberrant RNA splicing in cancer; expression changes and driver mutations of splicing factor genes". Oncogene. 35 (19): 2413- ... "Abnormal RNA splicing and genomic instability after induction of DNMT3A mutations by CRISPR/Cas9 gene editing". Blood Cells, ... For certain types of cancer, like in colorectal and prostate, the number of splicing errors per cancer has been shown to vary ... Transcriptome instability is a genome-wide, pre-mRNA splicing-related characteristic of certain cancers. In general, pre-mRNA ...

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

RNA splicing, Non-coding RNA). ... The unconventional splicing in this group results in excising ... Hooks KB, Griffiths-Jones S (2011). "Conserved RNA structures in the non-canonical Hac1/Xbp1 intron". RNA Biol. 8 (4): 552-556 ... doi:10.4161/rna.8.4.15396. PMC 3225973. PMID 21593604. Saloheimo M, Valkonen M, Penttila M (2003). "Activation mechanisms of ... Loop regions of the hairpins define the position of splice sites recognised by endoribonuclease Ire1 in response to ER stress. ...

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

This is accomplished through RNA splicing. The exons of these 25,000 genes can be spliced in many different ways to create ... SplitSeek allows de novo prediction of splice junctions in short-read RNA-seq data, suitable for detection of novel splicing ... CRAC integrates genomic locations and local coverage to enable splice junction or fusion RNA predictions directly from RNA-seq ... splicing reactions between a protein coding RNA and a universal sequence result in the attachment of a splice-leader to the 5' ...

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

Genetics databases, RNA splicing, Medical databases). ... "The RNA modification landscape in human disease". RNA: rna. ... This RNA modification databases are a compilation of databases and web portals and servers used for RNA modification. RNA ... doi:10.1261/rna.063503.117. PMC 5688997. Sun, WJ; Li, JH; Liu, S; Wu, J; Zhou, H; Qu, LH; Yang, JH (11 October 2015). "RMBase: ... It can affect the activity, localization as well as stability of RNAs, and has been linked with human cancer and diseases. Li, ...

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

Madocsai C, Lim SR, Geib T, Lam BJ, Hertel KJ (2005). "Correction of SMN2 Pre-mRNA splicing by antisense U7 small nuclear RNAs ... The U7 small nuclear RNA (U7 snRNA) is an RNA molecule and a component of the small nuclear ribonucleoprotein complex (U7 snRNP ... sequences of the sea urchin U7 small nuclear RNA suggest specific contacts between histone mRNA precursor and U7 RNA during RNA ... "Stable alteration of pre-mRNA splicing patterns by modified U7 small nuclear RNAs". Proc Natl Acad Sci U S A. 95 (9): 4929-4934 ...

https://en.wikipedia.org/wiki/U7_small_nuclear_RNA

... (snRNA) is a class of small RNA molecules that are found within the splicing speckles and Cajal bodies of the ... U1 spliceosomal RNA, U2 spliceosomal RNA, U4 spliceosomal RNA, U5 spliceosomal RNA, and U6 spliceosomal RNA. Their nomenclature ... Spliceosomes catalyse splicing, an integral step in eukaryotic precursor messenger RNA maturation. A splicing mistake in even a ... These are small RNA molecules that play an essential role in RNA biogenesis and guide chemical modifications of ribosomal RNAs ...

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

... these are called self-splicing RNAs. There are two main groups of self-splicing RNAs: group I catalytic intron and group II ... VegT RNA, Oskar RNA, ENOD40, p53 RNA and SR1 RNA. Bifunctional RNAs have recently been the subject of a special issue of ... "Sequence analysis of RNase MRP RNA reveals its origination from eukaryotic RNase P RNA". RNA. 12 (5): 699-706. doi:10.1261/rna. ... OxyS RNA is induced in response to oxidative stress in Escherichia coli.[citation needed] The B2 RNA is a small noncoding RNA ...

https://en.wikipedia.org/wiki/Non-coding_RNA

They also have small nuclear RNAs (snRNAs) involved in splicing pre-messenger RNA into messenger RNA in eukaryotic cells. 2 In ... She showed that yeast have small nuclear RNAs (snRNAs) involved in splicing pre-messenger RNA into messenger RNA in eukaryotic ... Strauss E. J., Guthrie C., 1991 "A cold-sensitive mRNA splicing mutant is a member of the RNA helicase gene family." Genes Dev ... Burgess S. M., Guthrie C., 1993 "A mechanism to enhance mRNA splicing fidelity: the RNA-dependent ATPase Prp16 governs usage of ...

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

April 2016). "RNA splicing is a primary link between genetic variation and disease". Science. 352 (6285): 600-4. Bibcode: ... Splicing quantitative trait loci (abbreviated sQTLs or splicing QTLs) are quantitative trait loci that regulate alternative ... splicing of pre-mRNA. They can be detected using RNA-seq data. Methods that have been developed to discover sQTLs include ... 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

Other strategies targeting the mutant pre-mRNA by exon skipping and/or spliceosome-mediated RNA trans-splicing (SMaRT) have ... Hammond SM, Wood MJ (May 2011). "Genetic therapies for RNA mis-splicing diseases". Trends in Genetics. 27 (5): 196-205. doi: ... 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 ...

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

Her research interests are in RNA splicing. In 1972 she married Dr Ian Beggs. They have two sons. She has been a Fellow of the ... "Jean Beggs: 2018 RNA Society Lifetime Achievement Award , RNA Society". Retrieved 28 June 2019. v t e (Articles with short ... In 2018 RNA Society Lifetime Achievement Award. Who's who (Online ed.). Oxford University Press. 2017. "Jean Beggs profile". ...

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

... effects on cellular RNA transport, splicing, translation. Anti-interferon protein. The "NS1 of the highly pathogenic avian H5N1 ... It encodes by using different reading frames from the same RNA segment. M1 is a protein that binds to the viral RNA. M2 is a ... and the PB1 avian flu virus RNA molecules with their genes combined with the remaining five RNA molecules (PB2, PA, NP, M, and ... segmented RNA viruses. "The influenza virus RNA polymerase is a multifunctional complex composed of the three viral proteins ...

https://en.wikipedia.org/wiki/H5N1_genetic_structure

PRPF8 Rna splicing Spliceosome Grainger RJ, Beggs JD (May 2005). "Prp8 protein: at the heart of the spliceosome". RNA. 11 (5): ... Prp8 is also more involved with maintaining proper conformation of the bound RNA cofactors and substrates of the splicing ... where it remains bound to the lariat before the spliced RNA is released and the snRNPs are recycled. Common research methods ... "Ubiquitin binding by a variant Jab1/MPN domain in the essential pre-mRNA splicing factor Prp8p". RNA. 12 (2): 292-302. doi: ...

https://en.wikipedia.org/wiki/Prp8

Site-selective RNA splicing nanozyme was developed. A nanozymes special issue in Progress in Biochemistry and Biophysics was ... "Site-Selective RNA Splicing Nanozyme: DNAzyme and RtcB Conjugates on a Gold Nanoparticle". ACS Chemical Biology. 13 (1): 215- ... Combined with small interfering RNA, ceria nanozyme was used for synergistic treatment of neurodegenerative diseases. A ... Catalytic Small Interfering RNA Nanocarriers for Synergistic Treatment of Neurodegenerative Diseases". Advanced Materials. 34 ( ...

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

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

Some of these are believed to affect the shape of nucleic acids (see for example RNA self-splicing), but this is only sometimes ...

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

Probable ATP-dependent RNA helicase DDX46 is an enzyme that in humans is encoded by the DDX46 gene. This gene encodes a member ... The protein encoded by this gene is a component of the 17S U2 snRNP complex; it plays an important role in pre-mRNA splicing. ... DEAD box proteins, characterized by the conserved motif Asp-Glu-Ala-Asp (DEAD), are putative RNA helicases. They are implicated ... "Prp5 bridges U1 and U2 snRNPs and enables stable U2 snRNP association with intron RNA". EMBO J. 23 (2): 376-85. doi:10.1038/sj. ...

https://en.wikipedia.org/wiki/DDX46

Multiple alternatively spliced transcript variants encoding distinct isoforms have been found for this gene, but the biological ... Hillman RT, Green RE, Brenner SE (2005). "An unappreciated role for RNA surveillance". Genome Biology. 5 (2): R8. doi:10.1186/ ... Bayascas JR, Yuste VJ, Solé C, Sánchez-López I, Segura MF, Perera R, Comella JX (May 2004). "Characterization of splice ... ICAD is encoded by alternatively spliced mRNAs which generate long (ICAD-L) and short (ICAD-S) forms of ICAD. Therefore, ICAD ...

https://en.wikipedia.org/wiki/Caspase-activated_DNase

A case-control study of hospitalized patients found that the blood plasma levels of CMTM5 protein and CMTM5 messenger RNA (i.e ... 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

"Specific binding of an exonic splicing enhancer by the pre-mRNA splicing factor SRp55". RNA. 4 (1): 11-23. PMC 1369592. PMID ... Tran Q, Roesser JR (February 2003). "SRp55 is a regulator of calcitonin/CGRP alternative RNA splicing". Biochemistry. 42 (4): ... The protein encoded by this gene is involved in mRNA splicing and may play a role in site selection in alternative splicing. ... "Entrez Gene: SFRS6 splicing factor, arginine/serine-rich 6". Zahler AM, Lane WS, Stolk JA, Roth MB (May 1992). "SR proteins: a ...

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

... is a Chinese biophysicist specializing in the fields of protein X-ray crystallography and RNA splicing. He was the Dean of ...

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

"The transcription elongation factor CA150 interacts with RNA polymerase II and the pre-mRNA splicing factor SF1". Mol. Cell. ... Multiple alternatively spliced transcript variants of this gene have been described, however, the full-length nature of many of ...

https://en.wikipedia.org/wiki/CDC25C

... domains that bind RNAs. This protein binds to the intronic polypyrimidine tracts that requires pre-mRNA splicing and acts via ... The hnRNPs are RNA-binding proteins and they complex with heterogeneous nuclear RNA (hnRNA). These proteins are associated with ... Conte MR, Grüne T, Ghuman J, Kelly G, Ladas A, Matthews S, Curry S (June 2000). "Structure of tandem RNA recognition motifs ... Alternatively spliced transcript variants encoding different isoforms have been described. In brains of mammals, transcripts ...

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

Three alternatively spliced transcript variants encoding different isoforms have been described for this gene. Caspase 10 has ... 1997). "A serine/arginine-rich nuclear matrix cyclophilin interacts with the C-terminal domain of RNA polymerase II". Nucleic ...

https://en.wikipedia.org/wiki/Caspase_10

Aberrant SON-mediated RNA splicing results from the accumulation of mis-spliced transcripts. The mis-spliced RNA products are ... SON is required for genome stability by ensuring the efficiency of RNA splicing of weak constitutive and alternative splice ... The SON gene is required for RNA splicing of transcripts encoding the cell-cycle protein TUBG1 and genes maintaining hESC ... Mutations in the SON gene and or SON haploinsufficiency compromises SON-mediated RNA splicing and contributes to the complex ...

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

"Entrez Gene: SFRS2IP splicing factor, arginine/serine-rich 2, interacting protein". Gui JF, Lane WS, Fu XD (1994). "A serine ... of RNA polymerase II through a conserved interaction domain". Biol Chem. 378 (6): 565-71. doi:10.1515/bchm.1997.378.6.565. PMID ... Zhang WJ, Wu JY (Feb 1998). "Sip1, a novel RS domain-containing protein essential for pre-mRNA splicing". Mol Cell Biol. 18 (2 ... kinase regulates intracellular localization of splicing factors in the cell cycle". Nature. 369 (6482): 678-82. Bibcode: ...

https://en.wikipedia.org/wiki/SFRS2IP

Splicing factor 3b, together with splicing factor 3a and a 12S RNA unit, forms the U2 small nuclear ribonucleoproteins complex ... RNA. 10 (2): 240-53. doi:10.1261/rna.5153204. PMC 1370536. PMID 14730023. Will CL, Schneider C, Hossbach M, Urlaub H, Rauhut R ... RNA. 10 (6): 929-41. doi:10.1261/rna.7320604. PMC 1370585. PMID 15146077. Beausoleil SA, Jedrychowski M, Schwartz D, Elias JE, ... Splicing factor 3B subunit 1 is a protein that in humans is encoded by the SF3B1 gene. This gene encodes subunit 1 of the ...

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

"Entrez Gene: RBMX RNA binding motif protein, X-linked". Hofmann Y, Wirth B (Aug 2002). "hnRNP-G promotes exon 7 inclusion of ... 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 ... RNA. 8 (4): 426-39. doi:10.1017/S1355838202021088. PMC 1370266. PMID 11991638. Hofmann Y, Wirth B (Aug 2002). "hnRNP-G promotes ...

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

RNA pseudogenes are reverse transcribed RNA genes). Pseudogenes are generally functionless as they descend from processed RNAs ... These dog-specific SINEs may code for a splice acceptor site, altering the sequences that appear as exons or introns in each ... For example, the 5' of the Alu sine is derived from 7SL RNA, a sequence transcribed by RNA Polymerase III which codes for the ... Short-interspersed nuclear elements are transcribed by RNA polymerase III which is known to transcribe ribosomal RNA and tRNA, ...

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

"Statistically based splicing detection reveals neural enrichment and tissue-specific induction of circular RNA during human ... C17orf78 has two splice variant isoforms. Isoform 1 is encoded by a mRNA sequence that is 1920 base pairs in length. Isoform 2 ... "RNAfold web server". rna.tbi.univie.ac.at. Retrieved 2020-05-21. "NetPhos 3.1 Server - prediction results". www.cbs.dtu.dk. ... "Gene: C17orf78 (ENSG00000278505) - Splice variants - Homo sapiens - Ensembl genome browser 100". uswest.ensembl.org. Retrieved ...

https://en.wikipedia.org/wiki/C17orf78

RNA splicing, and cellular differentiation. Ubiquitin itself was first discovered in the 1970s and originally named "ubiquitous ...

https://en.wikipedia.org/wiki/Ubiquitin-like_protein

2015). "SMN2 splice modulators enhance U1-pre-mRNA association and rescue SMA mice". Nature Chemical Biology. 11 (7): 511-7. ... RNA Complexation That Target the RNA: Specific Recognition of Human Immunodeficiency Virus Type 1 TAR RNA by Small Organic ... Additionally, HIV-1 RNA has been targeted extensively in vitro by RNA-binding small molecules. In 2007, Miller and coworkers ... An NMR structure of the RNA in complex with DB213, showed that the small molecule bound to the major groove of the RNA duplex. ...

https://en.wikipedia.org/wiki/RNA-targeting_small_molecule_drugs

Notable characteristics of trypanosomatids are the ability to perform trans-splicing of RNA and possession of glycosomes, where ...

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

... and RNA splicing. This gene encodes a protein which contains 2 WW domains and a coiled-coil region. It is ubiquitously ...

https://en.wikipedia.org/wiki/SAV1

Alternative splicing results in five different isoforms for this gene composed of any combination of six exons. C1orf194 is ... located near the KIAA1324 gene, poly(rC) binding protein 1 pseudogene, small Cajal body-specific RNA 2 gene, and the seryl-tRNA ...

https://en.wikipedia.org/wiki/Chromosome_1_open_reading_frame_194

1996). "The RNA 3' cleavage factors CstF 64 kDa and CPSF 100 kDa are concentrated in nuclear domains closely associated with ... McCracken S, Lambermon M, Blencowe BJ (2002). "SRm160 Splicing Coactivator Promotes Transcript 3′-End Cleavage". Mol. Cell. ... 2005). "Human Fip1 is a subunit of CPSF that binds to U-rich RNA elements and stimulates poly(A) polymerase". EMBO J. 23 (3): ... In most cases eukaryotic pre-messenger(m)RNA 3 prime ends are processed in two coordinated steps. First there is a site- ...

https://en.wikipedia.org/wiki/CPSF1

Zhang WJ, Wu JY (February 1998). "Sip1, a novel RS domain-containing protein essential for pre-mRNA splicing". Molecular and ... "A functional interaction between the survival motor neuron complex and RNA polymerase II". The Journal of Cell Biology. 152 (1 ... Aerbajinai W, Ishihara T, Arahata K, Tsukahara T (June 2002). "Increased expression level of the splicing variant of SIP1 in ...

https://en.wikipedia.org/wiki/Gem-associated_protein_2

Hachet, Olivier; Ephrussi, Anne (2004). "Splicing of oskar RNA in the nucleus is coupled to its cytoplasmic localization". ... RNA (since 2018) RNA -- Editors and Editorial Board Editorial Board, Journal of Cell Biology (since 2018) "Ephrussi Group - RNA ... WIREs RNA (since 2009) Editorial & Advisory Board - RNA - WIREs Home Editorial Board, Cell (since 2009) Editorial Board, ... RNA. 20 (4): 429-439. doi:10.1261/rna.041566.113. ISSN 1469-9001. PMC 3964905. PMID 24572808. Chekulaeva, Marina; Hentze, ...

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

"Efficient integration of an intron RNA into double-stranded DNA by reverse splicing". Nature. 381 (6580): 332-5. Bibcode: ... Goodrich-Blair H, Scarlato V, Gott JM, Xu M, Shub DA (October 1990). "A self-splicing group I intron in the DNA polymerase gene ... Mills DA, McKay LL, Dunny GM (June 1996). "Splicing of a group II intron involved in the conjugative transfer of pRS01 in ... Shearman C, Godon JJ, Gasson M (July 1996). "Splicing of a group II intron in a functional transfer gene of Lactococcus lactis ...

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

Mochizuki, Kazufumi (2010). "DNA rearrangements directed by non-coding RNAs in ciliates". Wiley Interdisciplinary Reviews: RNA ... are spliced together to give the operational gene. Tetrahymena has about 6,000 IESs and about 15% of micronuclear DNA is ... The process is guided by small RNAs and epigenetic chromatin marks. In spirotrich ciliates (such as Oxytricha), the process is ... The macronucleus provides the small nuclear RNA for vegetative growth. Division of the macronucleus occurs in most ciliate ...

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

Small nuclear RNA, Spliceosome, RNA splicing, All stub articles, Molecular and cellular biology stubs). ... Small Cajal body specific RNA 16 (also known as SCARNA16 or ACA47) is a small nucleolar RNA found in Cajal bodies and believed ... scaRNAs are a specific class of small nucleolar RNAs that localise to the Cajal bodies and guide the modification of RNA ... ACA47 belongs to the H/ACA box class of guide RNAs as it has the predicted hairpin-hinge-hairpin-tail structure, the conserved ...

https://en.wikipedia.org/wiki/Small_Cajal_body_specific_RNA_16

SXL regulates pre-messenger RNA in males to differentially splice MSLs and result in the appropriate increase in X chromosome ... Female embryos have an accumulation of Xist RNA on one of the two X chromosomes, beginning around the 8-cell stage. Xist RNA ... One example is MHM (male hypermethylated) RNA, an Xist-like long noncoding RNA that is expressed only in female chickens (ZW). ... Xist RNA is tightly associated with the Xi and it is required for X Chromosome Inactivation to occur in cis. Knockout studies ...

https://en.wikipedia.org/wiki/Sex-chromosome_dosage_compensation

Orphaned articles from July 2019, All orphaned articles, RNA splicing, Non-coding RNA). ... Hooks KB, Griffiths-Jones S (2011). "Conserved RNA structures in the non-canonical Hac1/Xbp1 intron". RNA Biol. 8 (4): 552-556 ... Splicing performed by Ire1 results in excision of a very long intron that was first described in Candida parapsilosis. ... doi:10.4161/rna.8.4.15396. PMC 3225973. PMID 21593604. Iracane, Elise; Donovan, Paul D.; Ola, Mihaela; Butler, Geraldine; ...

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

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

5 cap and poly-A tail. Splicing, introns, and exons.

https://www.khanacademy.org/science/biology/gene-expression-central-dogma/transcription-of-dna-into-rna/a/eukaryotic-pre-mrna-processing

These RNAs are called small nuclear RNAs (snRNAs) and theyre one example of a host of small RNAs produced by non-protein ... In the first step of the splicing reaction, the various components of the spliceosome bind to the 5′ splice site, the 3′ splice ... rnasplicing-geneexpression.blogspot.com/2009/12/gene-expression-and-rna-splicing.html ... For protein-encoding genes the splicing reactions are catalyzed by an RNA/protein complex called a spliceosome. In some cases, ...

https://sandwalk.blogspot.com/2007/06/rna-splicing-introns-and-exons.html

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 ... Tool for the detection and quantification of alternative splicing events from RNA-Seq data. ... Tool for the detection and quantification of alternative splicing events from RNA-Seq data. ...

https://github.com/ratschlab/spladder

Roivant makes a play in the emerging RNA splicing category, licensing rights to a drug developed by Eisai biotech unit H3 ... RNA splicing occurs when a precursor form of mRNA - which is used as a template for protein synthesis in cells - is transformed ... The RNA splicing approach has already been validated by Biogen with its spinal muscular atrophy blockbuster Spinraza ( ... Roivant is the latest pharma group to take a position in the emerging field of therapies targeted at RNA splicing, licensing ...

https://pharmaphorum.com/news/roivant-joins-rna-splicing-push-with-eisai-deal/

... many of which may regulate gene transcription or RNA splicing. To identify variants with regulatory functions in cattle, an ... that are associated with variations in the RNA splicing, i.e., sQTLs. To further the understanding of regulatory variants, ... Using whole genome and RNA sequence data from four tissues of over 200 cattle, sQTLs identified using exon inclusion ratios ... For many exons, the splicing and expression level was determined by the same cis additive genetic variance in different tissues ...

https://bmcgenomics.biomedcentral.com/articles/10.1186/s12864-018-4902-8/tables/2

Animal fashions have lengthy served as a foundation for scientific experimentation, biomedical analysis, drug growth and testing, illness modelling and toxicity research, as theyre extensively thought…. ...

https://www.gfme.org/tag/rna-splicing/

In this paper, we present a classification based approach for calling splicing junctions from RNA-seq data, which is ... such as the analysis of alternative splicing and isoform construction. However, because of the existence of introns, when RNA- ... It is an important step to align reads to the reference genome and call out splicing junctions for the following analysis, ... We compare SpliceJumper with two existing RNA-seq analysis approaches, TopHat2 and MapSplice2, on both simulated and real data ...

https://bmcbioinformatics.biomedcentral.com/articles/10.1186/1471-2105-16-S17-S10

Methods Eighteen MSH2 variants, mostly localised within canonical splice sites, were analysed by using minigene splicing assays ... Comprehensive RNA and protein functional assessments contribute to the clinical interpretation of MSH2 variants causing in- ... Comprehensive RNA and protein functional assessments contribute to the clinical interpretation of MSH2 variants causing in- ... Results Three in-frame RNA biotypes were identified based on variant-induced spliceogenic outcomes: exon skipping (E3, E4, E5 ...

https://jmg.bmj.com/content/early/2022/09/15/jmg-2022-108576

Trypanosome spliced leader RNA for diagnosis of acoziborole treatment outcome in gambiense human African trypanosomiasis: A ... Evaluation of a pan-Leishmania spliced-leader RNA detection method in human blood and experimentally infected Syrian golden ... A new RNA real-time quantitative PCR (qPCR) assay was developed targeting the conserved and highly expressed spliced-leader (SL ... The authors conclude that the single SL-RNA qPCR assay enables universal Leishmania detection and represents a particularly ...

https://dndi.org/scientific-articles/2018/evaluation-pan-leishmania-spliced-leader-rna-detection/

It appears that your browser has JavaScript disabled. Rosalind requires your browser to be JavaScript enabled ...

https://rosalind.info/problems/splc/recent/?page=3

Short Note on RNA Splicing Factors and RNA-Directed DNA Methylation. Research & Reviews is a scientific organization that ... Short Note on RNA Splicing Factors and RNA-Directed DNA Methylation. Abstract. RNA-Directed histone and additionally DNA ... The heterochromation formation in yeast is interceded by RNA- Directed hushing system, while the foundation of DNA methylation ... in plants is through the RNA-coordinated DNA methylation (RdDM) pathway. Recently, grafting factors are accounted for to be ...

https://www.rroij.com/peer-reviewed/short-note-on-rna-splicing-factors-and-rnadirected-dna-rnmethylation-90973.html

The portal, described in Nature Genetics, houses variant-related messenger RNA splicing insights drawn from RNA sequencing data ... SpliceVault Portal Provides Look at RNA Splicing Changes Linked to Genetic Variants ... in nearly 335,700 samples - a set known as the 300K-RNA resource. ...

https://www.genomeweb.com/dxpgx/alert-fda-s-pgx-guidance-delayed-until-end-summer

Tissue-specific splicing pattern of fibronectin messenger RNA precursor during development and aging in rat. Journal of Cell ... Tissue-specific splicing pattern of fibronectin messenger RNA precursor during development and aging in rat. In: Journal of ... Tissue-specific splicing pattern of fibronectin messenger RNA precursor during development and aging in rat. / Pagani, Franco; ... title = "Tissue-specific splicing pattern of fibronectin messenger RNA precursor during development and aging in rat", ...

https://moh-it.pure.elsevier.com/en/publications/tissue-specific-splicing-pattern-of-fibronectin-messenger-rna-pre

Our identification of spliced variants that are more specific for cancer than the full-length transcript has opened new ... In lung cancer patients, the osteopontin-c blood RNA levels had an increasing trend with tumor grade. Osteopontin-b and -c in ...

https://springerplus.springeropen.com/articles/10.1186/2193-1801-2-110/tables/1

RNA, Test Kits, Uncategorized, Vector & Virus, Western Blot ...

https://www.homocysteine.net/tag/rna-splicing/

Tag: rna splicing. alexa fluor secondary antibodies alexa488 Antibodies Assay Kits cDNA Clia Kits Culture Cells Devices Elisa ... Serums NATtrol p57 kip2 antibody Panel Particles PCR Pcr Kits Peptides Reagents Recombinant Proteins Ria Kits RNA Test Kits ... gentaur human igg antibody Isotypes lh elisa NATtrol p57 kip2 antibody Particles PCR Peptides Reagents Recombinant Proteins RNA ...

https://diastrip.com/tag/rna-splicing/

What is really one of the sequence and rna splicing lecture notes and taking of textbook chapters. ... Splicing and alternative splicing in rice and humans NCBI NIH. If males and rna splicing lecture notes quiz map, jurisica i ... In eukaryotic cells, studies of RNA splicing and alternative splicing in plants, three introns are removed from the RNA to ... You wish to rna splicing lecture notes on context of splicing factors, or lecture notes lesson central dogma of this? The part ...

https://babybminephotography.com/47587/rna_notes_splicing_7925_lecture.php

N2 - Spliceosome-mediated RNA trans-splicing (SMaRT) was investigated as a means for functionally correcting endogenous ΔF508 ... AB - Spliceosome-mediated RNA trans-splicing (SMaRT) was investigated as a means for functionally correcting endogenous ΔF508 ... Spliceosome-mediated RNA trans-splicing (SMaRT) was investigated as a means for functionally correcting endogenous ΔF508 cystic ... abstract = "Spliceosome-mediated RNA trans-splicing (SMaRT) was investigated as a means for functionally correcting endogenous ...

https://researchexperts.utmb.edu/en/publications/partial-correction-of-endogenous-%CE%B4f508-cftr-in-human-cystic-fibro

Splicing mechanism of group ll intron. Alternative Splicing. *Alternative splicing, also known as alternative RNA splicing or ... RNA Splicing Definition, Types, Mechanisms. What is RNA splicing? In order for mRNA to be translated into a protein, RNA ... What is RNA splicing?. In order for mRNA to be translated into a protein, RNA splicing removes the intervening, non-coding ... RNA Splicing Process is divided into 2 transesterification steps such as;. First Transesterification. *RNA splicing begins with ...

https://microbiologynote.com/rna-splicing-definition-types-mechanisms/

RNA Splicing and Aging RNA mini gene reporters using fluorescent proteins allow live imaging of alternative RNA splicing in ...

https://www.hsph.harvard.edu/mair-lab/

Self-Splicing" by people in this website by year, and whether "RNA, Ribosomal, Self-Splicing" was a major or minor topic of ... "RNA, Ribosomal, Self-Splicing" is a descriptor in the National Library of Medicines controlled vocabulary thesaurus, MeSH ( ... Below are the most recent publications written about "RNA, Ribosomal, Self-Splicing" by people in Profiles. ... Below are MeSH descriptors whose meaning is more general than "RNA, Ribosomal, Self-Splicing". ...

https://researchers.childrensmercy.org/display/24730

Dive into the research topics of recount3: summaries and queries for large-scale RNA-seq expression and splicing. Together ... recount3: summaries and queries for large-scale RNA-seq expression and splicing. ...

https://ohsu.pure.elsevier.com/en/publications/recount3-summaries-and-queries-for-large-scale-rna-seq-expression/fingerprints/

... transcript expression and alternative splicing. Key to this is the the accurate identification of... ... alternative splicing Earlham Institute Portcullis splice mapping splicing and junction mapping 2018-11-14 RNA-Seq Blog ... Portcullis - efficient and accurate detection of splice junctions from RNA-Seq. in Splicing and Junction Mapping November 14, ... What is RNA-Seq?. long RNAs are first converted into a library of cDNA fragments through either RNA fragmentation or DNA ...

https://www.rna-seqblog.com/portcullis-efficient-and-accurate-detection-of-splice-junctions-from-rna-seq/

... gelsyn-3 reagents coa reagents definition rna-seq rna definition rnai rna polymerase rnascope rnase rna structure rna virus rna ... UCLA Researchers use RNA Import to Compensate for Mutations in Human Mitochondrial DNA ...

https://teitell-lab.com/tag/rna-splicing/

What is alternative RNA splicing? asked in Molecular Basis of Inheritance by Lifeeasy Biology *. molecular-basis-of-inheritance ... What are the chemical differences between DNA and RNA? asked in Molecular Basis of Inheritance by Lifeeasy Biology *. molecular ...

http://www.biology.lifeeasy.org/2315/what-happens-during-rna-splicing

Hu J, Khodadadi-Jamayran A, Mao M et al (2016) AKAP95 regulates splicing through scaffolding RNAs and RNA processing factors. ... AKAP95; Splicing; RNA processing; Rights. © 2016 Hu J et al. This work is licensed under a CC BY license (Creative Commons ... and support a model that AKAP95 facilitates the splice site communication by looping out introns through both RNA-binding and ... and functionally regulates pre-mRNA splicing. AKAP95 directly promotes splicing in vitro and the inclusion of a specific exon ...

https://bradscholars.brad.ac.uk/handle/10454/10168

Model demonstrates how RNA splicing defects contribute to Alzheimers disease. Researchers have puzzled over the ...

https://www.lifetechnology.com/blogs/life-technology-medical-news/model-demonstrates-how-rna-splicing-defects-contribute-to-alzheimers-disease

... May 27, 2016 09:00 AM - 10:00 AM Hutchison Hall 473 ...

http://www.sas.rochester.edu/chm/news-events/events/2016/05/amelioration-of-a-disease-state-by-small-molecule-rna-splicing-modulators.html

During the past 10years, genetic therapy directed toward correction of RNA mis-splicing in disease has progressed from ... splicing to treat Duchenne muscular dystrophy opens the door for the use of splicing modification for most of the mis-splicing ... trans-splicing and modification of U1 and U7 snRNA to target splice sites. The success of clinical trials for modifying ... In this review, we discuss the use of antisense oligonucleotides to modify splicing as well as the principles and latest work ...

https://www.stemcells.ox.ac.uk/publications/134947

Anatomy16

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Diseases1

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JNK2 is required for efficient T-cell activation and apoptosis but not for normal lymphocyte development. (1/7106)

In vivo expression of the nucleolar group I intron-encoded I-dirI homing endonuclease involves the removal of a spliceosomal intron. (2/7106)

The splicing factor-associated protein, p32, regulates RNA splicing by inhibiting ASF/SF2 RNA binding and phosphorylation. (3/7106)

Tight binding of the 5' exon to domain I of a group II self-splicing intron requires completion of the intron active site. (4/7106)

A premature termination codon interferes with the nuclear function of an exon splicing enhancer in an open reading frame-dependent manner. (5/7106)

Substrate specificities of SR proteins in constitutive splicing are determined by their RNA recognition motifs and composite pre-mRNA exonic elements. (6/7106)

Alterations in the conserved SL1 trans-spliced leader of Caenorhabditis elegans demonstrate flexibility in length and sequence requirements in vivo. (7/7106)

A novel genetic screen for snRNP assembly factors in yeast identifies a conserved protein, Sad1p, also required for pre-mRNA splicing. (8/7106)

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RNA

RNA, Small Interfering

RNA, Viral

RNA Editing

RNA Splicing

RNA, Ribosomal

RNA, Bacterial

DNA-Directed RNA Polymerases

RNA Viruses

RNA Interference

RNA, Messenger

RNA, Double-Stranded

RNA, Catalytic

RNA Folding

RNA Polymerase II

RNA, Fungal

RNA Stability

RNA Helicases

RNA, Antisense

RNA Processing, Post-Transcriptional

RNA, Transfer

RNA, Small Nuclear

RNA Precursors

RNA, Untranslated

Nucleic Acid Conformation

RNA Caps

Sequence Analysis, RNA

RNA, Plant

RNA, Protozoan

Base Sequence

RNA, Neoplasm

RNA Ligase (ATP)

DEAD-box RNA Helicases

RNA Polymerase III

Molecular Sequence Data

RNA Polymerase I

RNA, Nuclear

RNA, Guide

RNA, Ribosomal, 28S

RNA, Ribosomal, 18S

RNA-Binding Proteins

RNA, Ribosomal, 23S

RNA Transport

RNA, Spliced Leader

RNA, Satellite

RNA, Ribosomal, 16S

Amino Acid Sequence

RNA, Archaeal

Nucleic Acid Hybridization

Protein Biosynthesis

Cell Line

Virus Replication

Escherichia coli

RNA Cleavage

Mutation

Oligoribonucleotides

RNA, Heterogeneous Nuclear

Transcription, Genetic

RNA, Small Cytoplasmic

RNA 3' End Processing

Templates, Genetic

RNA, Small Untranslated

HeLa Cells

Ribonucleoproteins

Ribonucleases

Poly A

Genome, Viral

RNA, Ribosomal, 5.8S

DNA

RNA, Long Noncoding

RNA, Small Nucleolar

Binding Sites

RNA Virus Infections

Protein Binding

RNA, Complementary

Uridine

Promoter Regions, Genetic

Endoribonucleases

Cell Nucleus

RNA, Chloroplast