Nucleotide sequences located at the ends of EXONS and recognized in pre-messenger RNA by SPLICEOSOMES. They are joined during the RNA SPLICING reaction, forming the junctions between exons.
The ultimate exclusion of nonsense sequences or intervening sequences (introns) before the final RNA transcript is sent to the cytoplasm.
The sequence of PURINES and PYRIMIDINES in nucleic acids and polynucleotides. It is also called nucleotide sequence.
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.
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 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.
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.
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.
The parts of a transcript of a split GENE remaining after the INTRONS are removed. They are spliced together to become a MESSENGER RNA or other functional RNA.
A 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)
Ribonucleic acid that makes up the genetic material of viruses.
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.
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.
Organelles in which the splicing and excision reactions that remove introns from precursor messenger RNA molecules occur. One component of a spliceosome is five small nuclear RNA molecules (U1, U2, U4, U5, U6) that, working in conjunction with proteins, help to fold pieces of RNA into the right shapes and later splice them into the message.
A nuclear RNA-protein complex that plays a role in RNA processing. In the nucleoplasm, the U1 snRNP along with other small nuclear ribonucleoproteins (U2, U4-U6, and U5) assemble into SPLICEOSOMES that remove introns from pre-mRNA by splicing. The U1 snRNA forms base pairs with conserved sequence motifs at the 5'-splice site and recognizes both the 5'- and 3'-splice sites and may have a fundamental role in aligning the two sites for the splicing reaction.
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).
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.
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)
Proteins that bind to RNA molecules. Included here are RIBONUCLEOPROTEINS and other proteins whose function is to bind specifically to RNA.
Ribonucleic acid in fungi having regulatory and catalytic roles as well as involvement in protein synthesis.
Complexes of RNA-binding proteins with ribonucleic acids (RNA).
Ribonucleic acid in bacteria having regulatory and catalytic roles as well as involvement in protein synthesis.
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.
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).
The spatial arrangement of the atoms of a nucleic acid or polynucleotide that results in its characteristic 3-dimensional shape.
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.
A nuclear RNA-protein complex that plays a role in RNA processing. In the nucleoplasm, the U5 snRNP along with U4-U6 snRNP preassemble into a single 25S particle that binds to the U1 and U2 snRNPs and the substrate to form SPLICEOSOMES.
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.
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.
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).
A nuclear RNA-protein complex that plays a role in RNA processing. In the nucleoplasm, the U2 snRNP along with other small nuclear ribonucleoproteins (U1, U4-U6, and U5) assemble into SPLICEOSOMES that remove introns from pre-mRNA by splicing. The U2 snRNA forms base pairs with conserved sequence motifs at the branch point, which associates with a heat- and RNAase-sensitive factor in an early step of splicing.
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.
Viruses whose genetic material is RNA.
Different forms of a protein that may be produced from different GENES, or from the same gene by ALTERNATIVE SPLICING.
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.
Biochemical identification of mutational changes in a nucleotide sequence.
Use for nucleic acid precursors in general or for which there is no specific heading.
A class of closely related heterogeneous-nuclear ribonucleoproteins of approximately 34-40 kDa in size. Although they are generally found in the nucleoplasm, they also shuttle between the nucleus and the cytoplasm. Members of this class have been found to have a role in mRNA transport, telomere biogenesis and RNA SPLICING.
A family of proteins that promote unwinding of RNA during splicing and translation.
A multistage process that includes cloning, physical mapping, subcloning, sequencing, and information analysis of an RNA SEQUENCE.
The biosynthesis of RNA carried out on a template of DNA. The biosynthesis of DNA from an RNA template is called REVERSE TRANSCRIPTION.
A group of closely-related heterogeneous-nuclear ribonucleoproteins that are involved in pre-mRNA splicing.
A nuclear RNA-protein complex that plays a role in RNA processing. In the nucleoplasm, the U4-U6 snRNP along with the U5 snRNP preassemble into a single 25S particle that binds to the U1 and U2 snRNPs and the substrate to form mature SPLICEOSOMES. There is also evidence for the existence of individual U4 or U6 snRNPs in addition to their organization as a U4-U6 snRNP.
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 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
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.
A mutation caused by the substitution of one nucleotide for another. This results in the DNA molecule having a change in a single base pair.
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.
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.
The processes of RNA tertiary structure formation.
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.
Established cell cultures that have the potential to propagate indefinitely.
The parts of a macromolecule that directly participate in its specific combination with another molecule.
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.
Ribonucleic acid in plants having regulatory and catalytic roles as well as involvement in protein synthesis.
Theoretical representations that simulate the behavior or activity of genetic processes or phenomena. They include the use of mathematical equations, computers, and other electronic equipment.
The 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.
Ribonucleic acid in protozoa having regulatory and catalytic roles as well as involvement in protein synthesis.
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.
Short sequences (generally about 10 base pairs) of DNA that are complementary to sequences of messenger RNA and allow reverse transcriptases to start copying the adjacent sequences of mRNA. Primers are used extensively in genetic and molecular biology techniques.
The sequential correspondence of nucleotides in one nucleic acid molecule with those of another nucleic acid molecule. Sequence homology is an indication of the genetic relatedness of different organisms and gene function.
A theoretical representative nucleotide or amino acid sequence in which each nucleotide or amino acid is the one which occurs most frequently at that site in the different sequences which occur in nature. The phrase also refers to an actual sequence which approximates the theoretical consensus. A known CONSERVED SEQUENCE set is represented by a consensus sequence. Commonly observed supersecondary protein structures (AMINO ACID MOTIFS) are often formed by conserved sequences.
A 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.
The record of descent or ancestry, particularly of a particular condition or trait, indicating individual family members, their relationships, and their status with respect to the trait or condition.
A variation of the PCR technique in which cDNA is made from RNA via reverse transcription. The resultant cDNA is then amplified using standard PCR protocols.
A superfamily of proteins containing the globin fold which is composed of 6-8 alpha helices arranged in a characterstic HEME enclosing structure.
A deoxyribonucleotide polymer that is the primary genetic material of all cells. Eukaryotic and prokaryotic organisms normally contain DNA in a double-stranded state, yet several important biological processes transiently involve single-stranded regions. DNA, which consists of a polysugar-phosphate backbone possessing projections of purines (adenine and guanine) and pyrimidines (thymine and cytosine), forms a double helix that is held together by hydrogen bonds between these purines and pyrimidines (adenine to thymine and guanine to cytosine).
The 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.
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 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.
Deletion of sequences of nucleic acids from the genetic material of an individual.
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 multistage process that includes cloning, physical mapping, subcloning, determination of the DNA SEQUENCE, and information analysis.
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)
A sequence of amino acids in a polypeptide or of nucleotides in DNA or RNA that is similar across multiple species. A known set of conserved sequences is represented by a CONSENSUS SEQUENCE. AMINO ACID MOTIFS are often composed of conserved sequences.
The joining of RNA from two different genes. One type of trans-splicing is the "spliced leader" type (primarily found in protozoans such as trypanosomes and in lower invertebrates such as nematodes) which results in the addition of a capped, noncoding, spliced leader sequence to the 5' end of mRNAs. Another type of trans-splicing is the "discontinuous group II introns" type (found in plant/algal chloroplasts and plant mitochondria) which results in the joining of two independently transcribed coding sequences. Both are mechanistically similar to conventional nuclear pre-mRNA cis-splicing. Mammalian cells are also capable of trans-splicing.
A type of mutation in which a number of NUCLEOTIDES deleted from or inserted into a protein coding sequence is not divisible by three, thereby causing an alteration in the READING FRAMES of the entire coding sequence downstream of the mutation. These mutations may be induced by certain types of MUTAGENS or may occur spontaneously.
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
The insertion of recombinant DNA molecules from prokaryotic and/or eukaryotic sources into a replicating vehicle, such as a plasmid or virus vector, and the introduction of the resultant hybrid molecules into recipient cells without altering the viability of those cells.
RNA present in neoplastic tissue.
A category of nucleic acid sequences that function as units of heredity and which code for the basic instructions for the development, reproduction, and maintenance of organisms.
The 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.
Sequences within RNA that regulate the processing, stability (RNA STABILITY) or translation (TRANSLATION, GENETIC) of RNA.
Nucleic acid sequences that are involved in the negative regulation of GENETIC TRANSCRIPTION by chromatin silencing.
Pairing of purine and pyrimidine bases by HYDROGEN BONDING in double-stranded DNA or RNA.
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).
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.
Nucleic acid sequences involved in regulating the expression of genes.
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.
An amino acid-specifying codon that has been converted to a stop codon (CODON, TERMINATOR) by mutation. Its occurance is abnormal causing premature termination of protein translation and results in production of truncated and non-functional proteins. A nonsense mutation is one that converts an amino acid-specific codon to a stop codon.
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.
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.
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.
A naturally occurring furocoumarin, found in PSORALEA. After photoactivation with UV radiation, it binds DNA via single and double-stranded cross-linking.
The relative amounts of the PURINES and PYRIMIDINES in a nucleic acid.
The degree of similarity between sequences of amino acids. This information is useful for the analyzing genetic relatedness of proteins and species.
Cis-acting DNA sequences which can increase transcription of genes. Enhancers can usually function in either orientation and at various distances from a promoter.
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.
The outward appearance of the individual. It is the product of interactions between genes, and between the GENOTYPE and the environment.
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.
Variant forms of the same gene, occupying the same locus on homologous CHROMOSOMES, and governing the variants in production of the same gene product.
The arrangement of two or more amino acid or base sequences from an organism or organisms in such a way as to align areas of the sequences sharing common properties. The degree of relatedness or homology between the sequences is predicted computationally or statistically based on weights assigned to the elements aligned between the sequences. This in turn can serve as a potential indicator of the genetic relatedness between the organisms.
A 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.
Reagents with two reactive groups, usually at opposite ends of the molecule, that are capable of reacting with and thereby forming bridges between side chains of amino acids in proteins; the locations of naturally reactive areas within proteins can thereby be identified; may also be used for other macromolecules, like glycoproteins, nucleic acids, or other.
Detection of RNA that has been electrophoretically separated and immobilized by blotting on nitrocellulose or other type of paper or nylon membrane followed by hybridization with labeled NUCLEIC ACID PROBES.
The biosynthesis of PEPTIDES and PROTEINS on RIBOSOMES, directed by MESSENGER RNA, via TRANSFER RNA that is charged with standard proteinogenic AMINO ACIDS.
Databases containing information about NUCLEIC ACIDS such as BASE SEQUENCE; SNPS; NUCLEIC ACID CONFORMATION; and other properties. Information about the DNA fragments kept in a GENE LIBRARY or GENOMIC LIBRARY is often maintained in DNA databases.
The sequence at the 3' end of messenger RNA that does not code for product. This region contains transcription and translation regulating sequences.
Widely used technique which exploits the ability of complementary sequences in single-stranded DNAs or RNAs to pair with each other to form a double helix. Hybridization can take place between two complimentary DNA sequences, between a single-stranded DNA and a complementary RNA, or between two RNA sequences. The technique is used to detect and isolate specific sequences, measure homology, or define other characteristics of one or both strands. (Kendrew, Encyclopedia of Molecular Biology, 1994, p503)
A 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
Use of restriction endonucleases to analyze and generate a physical map of genomes, genes, or other segments of DNA.
A field of biology concerned with the development of techniques for the collection and manipulation of biological data, and the use of such data to make biological discoveries or predictions. This field encompasses all computational methods and theories for solving biological problems including manipulation of models and datasets.
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.
Any of the processes by which cytoplasmic factors influence the differential control of gene action in viruses.
A mutation in which a codon is mutated to one directing the incorporation of a different amino acid. This substitution may result in an inactive or unstable product. (From A Dictionary of Genetics, King & Stansfield, 5th ed)
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).
A RNA-binding protein that binds to polypyriminidine rich regions in the INTRONS of messenger RNAs. Polypyrimidine tract-binding protein may be involved in regulating the ALTERNATIVE SPLICING of mRNAs since its presence on an intronic RNA region that is upstream of an EXON inhibits the splicing of the exon into the final mRNA product.
Genetically engineered MUTAGENESIS at a specific site in the DNA molecule that introduces a base substitution, or an insertion or deletion.
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
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.
RNA molecules found in the nucleus either associated with chromosomes or in the nucleoplasm.
Trans-acting nuclear proteins whose functional expression are required for retroviral replication. Specifically, the rev gene products are required for processing and translation of the gag and env mRNAs, and thus rev regulates the expression of the viral structural proteins. rev can also regulate viral regulatory proteins. A cis-acting antirepression sequence (CAR) in env, also known as the rev-responsive element (RRE), is responsive to the rev gene product. rev is short for regulator of virion.
The acidic subunit of beta-crystallins.
Endogenous substances, usually proteins, which are effective in the initiation, stimulation, or termination of the genetic transcription process.
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)
An individual having different alleles at one or more loci regarding a specific character.
The process of cumulative change at the level of DNA; RNA; and PROTEINS, over successive generations.
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.
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.-.
Genotypic differences observed among individuals in a population.
Constituent of the 60S subunit of eukaryotic ribosomes. 28S rRNA is involved in the initiation of polypeptide synthesis in eukaryotes.
Process of generating a genetic MUTATION. It may occur spontaneously or be induced by MUTAGENS.
The phenotypic manifestation of a gene or genes by the processes of GENETIC TRANSCRIPTION and GENETIC TRANSLATION.
Proteins encoded by the REV GENES of the HUMAN IMMUNODEFICIENCY VIRUS.
A genus of ciliate protozoa commonly used in genetic, cytological, and other research.
Partial cDNA (DNA, COMPLEMENTARY) sequences that are unique to the cDNAs from which they were derived.
DNA sequences that form the coding region for a protein that regulates the expression of the viral structural and regulatory proteins in human immunodeficiency virus (HIV). rev is short for regulator of virion.
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.
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.
Any method used for determining the location of and relative distances between genes on a chromosome.

Identification of the alpha-aminoadipic semialdehyde synthase gene, which is defective in familial hyperlysinemia. (1/1146)

The first two steps in the mammalian lysine-degradation pathway are catalyzed by lysine-ketoglutarate reductase and saccharopine dehydrogenase, respectively, resulting in the conversion of lysine to alpha-aminoadipic semialdehyde. Defects in one or both of these activities result in familial hyperlysinemia, an autosomal recessive condition characterized by hyperlysinemia, lysinuria, and variable saccharopinuria. In yeast, lysine-ketoglutarate reductase and saccharopine dehydrogenase are encoded by the LYS1 and LYS9 genes, respectively, and we searched the available sequence databases for their human homologues. We identified a single cDNA that encoded an apparently bifunctional protein, with the N-terminal half similar to that of yeast LYS1 and with the C-terminal half similar to that of yeast LYS9. This bifunctional protein has previously been referred to as "alpha-aminoadipic semialdehyde synthase," and we have tentatively designated this gene "AASS." The AASS cDNA contains an open reading frame of 2,781 bp predicted to encode a 927-amino-acid-long protein. The gene has been sequenced and contains 24 exons scattered over 68 kb and maps to chromosome 7q31.3. Northern blot analysis revealed the presence of several transcripts in all tissues examined, with the highest expression occurring in the liver. We sequenced the genomic DNA from a single patient with hyperlysinemia (JJa). The patient is the product of a consanguineous mating and is homozygous for an out-of-frame 9-bp deletion in exon 15, which results in a premature stop codon at position 534 of the protein. On the basis of these and other results, we propose that AASS catalyzes the first two steps of the major lysine-degradation pathway in human cells and that inactivating mutations in the AASS gene are a cause of hyperlysinemia.  (+info)

A comprehensive survey of sequence variation in the ABCA4 (ABCR) gene in Stargardt disease and age-related macular degeneration. (2/1146)

Stargardt disease (STGD) is a common autosomal recessive maculopathy of early and young-adult onset and is caused by alterations in the gene encoding the photoreceptor-specific ATP-binding cassette (ABC) transporter (ABCA4). We have studied 144 patients with STGD and 220 unaffected individuals ascertained from the German population, to complete a comprehensive, population-specific survey of the sequence variation in the ABCA4 gene. In addition, we have assessed the proposed role for ABCA4 in age-related macular degeneration (AMD), a common cause of late-onset blindness, by studying 200 affected individuals with late-stage disease. Using a screening strategy based primarily on denaturing gradient gel electrophoresis, we have identified in the three study groups a total of 127 unique alterations, of which 90 have not been previously reported, and have classified 72 as probable pathogenic mutations. Of the 288 STGD chromosomes studied, mutations were identified in 166, resulting in a detection rate of approximately 58%. Eight different alleles account for 61% of the identified disease alleles, and at least one of these, the L541P-A1038V complex allele, appears to be a founder mutation in the German population. When the group with AMD and the control group were analyzed with the same methodology, 18 patients with AMD and 12 controls were found to harbor possible disease-associated alterations. This represents no significant difference between the two groups; however, for detection of modest effects of rare alleles in complex diseases, the analysis of larger cohorts of patients may be required.  (+info)

Restoration of correct splicing of thalassemic beta-globin pre-mRNA by modified U1 snRNAs. (3/1146)

The T-->G mutation at nucleotide 705 in the second intron of the beta-globin gene creates an aberrant 5' splice site and activates a 3' cryptic splice site upstream from the mutation. As a result, the IVS2-705 pre-mRNA is spliced via the aberrant splice sites leading to a deficiency of beta-globin mRNA and protein and to the genetic blood disorder thalassemia. We have shown previously that in cell culture models of thalassemia, aberrant splicing of beta-thalassemic IVS2-705 pre-mRNA was permanently corrected by a modified murine U7 snRNA that incorporated sequences antisense to the splice sites activated by the mutation. To explore the possibility of using other snRNAs as vectors for antisense sequences, U1 snRNA was modified in a similar manner. Replacement of the U1 9-nucleotide 5' splice site recognition sequence with nucleotides complementary to the aberrant 5' splice site failed to correct splicing of IVS2-705 pre-mRNA. In contrast, U1 snRNA targeted to the cryptic 3' splice site was effective. A hybrid with a modified U7 snRNA gene under the control of the U1 promoter and terminator sequences resulted in the highest levels of correction (up to 70%) in transiently and stably transfected target cells.  (+info)

Distinct mutations in the receptor tyrosine kinase gene ROR2 cause brachydactyly type B. (4/1146)

Brachydactyly type B (BDB) is an autosomal dominant skeletal disorder characterized by hypoplasia/aplasia of distal phalanges and nails. Recently, heterozygous mutations of the orphan receptor tyrosine kinase (TK) ROR2, located within a distinct segment directly after the TK domain, have been shown to be responsible for BDB. We report four novel mutations in ROR2 (two frameshifts, one splice mutation, and one nonsense mutation) in five families with BDB. The mutations predict truncation of the protein within two distinct regions immediately before and after the TK domain, resulting in a complete or partial loss of the intracellular portion of the protein. Patients affected with the distal mutations have a more severe phenotype than do those with the proximal mutation. Our analysis includes the first description of homozygous BDB in an individual with a 5-bp deletion proximal to the TK domain. His phenotype resembles an extreme form of brachydactyly, with extensive hypoplasia of the phalanges and metacarpals/metatarsals and absence of nails. In addition, he has vertebral anomalies, brachymelia of the arms, and a ventricular septal defect-features that are reminiscent of Robinow syndrome, which has also been shown to be caused by mutations in ROR2. The BDB phenotype, as well as the location and the nature of the BDB mutations, suggests a specific mutational effect that cannot be explained by simple haploinsufficiency and that is distinct from that in Robinow syndrome.  (+info)

Mutation analysis of Korean patients with citrullinemia. (5/1146)

Citrullinemia is an autosomal recessive disease due to the mutations in the argininosuccinate synthetase (ASS) gene. Mutation analysis was performed on three Korean patients with citrullinemia. All of the three patients had the splicing mutation previously reported as IVS6-2A>G mutation. Two had Gly324Ser mutation and the other patient had a 67-bp insertion mutation in exon 15. The IVS6-2A>G mutation was reported to be found frequently in Japanese patients with citrullinemia, but Caucasian patients showed the extreme mutational heterogeneity. Although a limited number of Korean patients were studied, the IVS6-2A>G mutation appears to be one of the most frequent mutant alleles in Korean patients with citrullinemia. The Gly324Ser mutation identified in two patients also suggests the possible high frequency of this mutation in Korean patients as well.  (+info)

Haploinsufficiency of ALX4 as a potential cause of parietal foramina in the 11p11.2 contiguous gene-deletion syndrome. (6/1146)

Heterozygous mutations in MSX2 are responsible for an autosomal dominant form of parietal foramina (PFM). PFM are oval defects of the parietal bones that are also a characteristic feature of a contiguous gene-deletion syndrome caused by a proximal deletion in the short arm of chromosome 11 (Potocki-Shaffer syndrome). We have identified a human bacterial artificial chromosome (BAC) clone mapping to chromosome 11, containing a region homologous to the human homeobox gene MSX2. Further sequence analysis demonstrated that the human orthologue (ALX4) of the mouse Aristaless-like 4 gene (Alx4) is contained within this 11p clone. We used FISH to test for the presence-or for the heterozygous deletion-of this clone in two patients with the 11p11.2-deletion syndrome and showed that this clone is deleted in these patients. ALX4 and Alx4 were shown to be expressed in bone and to be absent from all other tissues tested. The involvement of Alx4 in murine skull development, its bone-specific expression pattern, the fact that Alx4 is a dosage-sensitive gene in mice, and the localization of a human genomic clone containing ALX4 to 11p11.2, with hemizygosity in patients with deletion of 11p11.2 who have biparietal foramina, support the contention that ALX4 is a candidate gene for the PFM in the 11p11.2-deletion syndrome.  (+info)

Utilization of the bovine papillomavirus type 1 late-stage-specific nucleotide 3605 3' splice site is modulated by a novel exonic bipartite regulator but not by an intronic purine-rich element. (7/1146)

Bovine papillomavirus type 1 (BPV-1) late gene expression is regulated at both transcriptional and posttranscriptional levels. Maturation of the capsid protein (L1) pre-mRNA requires a switch in 3' splice site utilization. This switch involves activation of the nucleotide (nt) 3605 3' splice site, which is utilized only in fully differentiated keratinocytes during late stages of the virus life cycle. Our previous studies of the mechanisms that regulate BPV-1 alternative splicing identified three cis-acting elements between these two splice sites. Two purine-rich exonic splicing enhancers, SE1 and SE2, are essential for preferential utilization of the nt 3225 3' splice site at early stages of the virus life cycle. Another cis-acting element, exonic splicing suppressor 1 (ESS1), represses use of the nt 3225 3' splice site. In the present study, we investigated the late-stage-specific nt 3605 3' splice site and showed that it has suboptimal features characterized by a nonconsensus branch point sequence and a weak polypyrimidine track with interspersed purines. In vitro and in vivo experiments showed that utilization of the nt 3605 3' splice site was not affected by SE2, which is intronically located with respect to the nt 3605 3' splice site. The intronic location and sequence composition of SE2 are similar to those of the adenovirus IIIa repressor element, which has been shown to inhibit use of a downstream 3' splice site. Further studies demonstrated that the nt 3605 3' splice site is controlled by a novel exonic bipartite element consisting of an AC-rich exonic splicing enhancer (SE4) and an exonic splicing suppressor (ESS2) with a UGGU motif. Functionally, this newly identified bipartite element resembles the bipartite element composed of SE1 and ESS1. SE4 also functions on a heterologous 3' splice site. In contrast, ESS2 functions as an exonic splicing suppressor only in a 3'-splice-site-specific and enhancer-specific manner. Our data indicate that BPV-1 splicing regulation is very complex and is likely to be controlled by multiple splicing factors during keratinocyte differentiation.  (+info)

Selection of alternative 5' splice sites: role of U1 snRNP and models for the antagonistic effects of SF2/ASF and hnRNP A1. (8/1146)

The first component known to recognize and discriminate among potential 5' splice sites (5'SSs) in pre-mRNA is the U1 snRNP. However, the relative levels of U1 snRNP binding to alternative 5'SSs do not necessarily determine the splicing outcome. Strikingly, SF2/ASF, one of the essential SR protein-splicing factors, causes a dose-dependent shift in splicing to a downstream (intron-proximal) site, and yet it increases U1 snRNP binding at upstream and downstream sites simultaneously. We show here that hnRNP A1, which shifts splicing towards an upstream 5'SS, causes reduced U1 snRNP binding at both sites. Nonetheless, the importance of U1 snRNP binding is shown by proportionality between the level of U1 snRNP binding to the downstream site and its use in splicing. With purified components, hnRNP A1 reduces U1 snRNP binding to 5'SSs by binding cooperatively and indiscriminately to the pre-mRNA. Mutations in hnRNP A1 and SF2/ASF show that the opposite effects of the proteins on 5'SS choice are correlated with their effects on U1 snRNP binding. Cross-linking experiments show that SF2/ASF and hnRNP A1 compete to bind pre-mRNA, and we conclude that this competition is the basis of their functional antagonism; SF2/ASF enhances U1 snRNP binding at all 5'SSs, the rise in simultaneous occupancy causing a shift in splicing towards the downstream site, whereas hnRNP A1 interferes with U1 snRNP binding such that 5'SS occupancy is lower and the affinities of U1 snRNP for the individual sites determine the site of splicing.  (+info)

RNA splice sites are specific sequences on the pre-messenger RNA (pre-mRNA) molecule where the splicing process occurs during gene expression in eukaryotic cells. The pre-mRNA contains introns and exons, which are non-coding and coding regions of the RNA, respectively.

The splicing process removes the introns and joins together the exons to form a mature mRNA molecule that can be translated into a protein. The splice sites are recognized by the spliceosome, a complex of proteins and small nuclear RNAs (snRNAs) that catalyze the splicing reaction.

There are two main types of splice sites: the 5' splice site and the 3' splice site. The 5' splice site is located at the junction between the 5' end of the intron and the 3' end of the exon, while the 3' splice site is located at the junction between the 3' end of the intron and the 5' end of the exon.

The 5' splice site contains a conserved GU sequence, while the 3' splice site contains a conserved AG sequence. These sequences are recognized by the snRNAs in the spliceosome, which bind to them and facilitate the splicing reaction.

Mutations or variations in RNA splice sites can lead to abnormal splicing and result in diseases such as cancer, neurodegenerative disorders, and genetic disorders.

RNA splicing is a post-transcriptional modification process in which the non-coding sequences (introns) are removed and the coding sequences (exons) are joined together in a messenger RNA (mRNA) molecule. This results in a continuous mRNA sequence that can be translated into a single protein. Alternative splicing, where different combinations of exons are included or excluded, allows for the creation of multiple proteins from a single gene.

A base sequence in the context of molecular biology refers to the specific order of nucleotides in a DNA or RNA molecule. In DNA, these nucleotides are adenine (A), guanine (G), cytosine (C), and thymine (T). In RNA, uracil (U) takes the place of thymine. The base sequence contains genetic information that is transcribed into RNA and ultimately translated into proteins. It is the exact order of these bases that determines the genetic code and thus the function of the DNA or RNA molecule.

Messenger RNA (mRNA) is a type of RNA (ribonucleic acid) that carries genetic information copied from DNA in the form of a series of three-base code "words," each of which specifies a particular amino acid. This information is used by the cell's machinery to construct proteins, a process known as translation. After being transcribed from DNA, mRNA travels out of the nucleus to the ribosomes in the cytoplasm where protein synthesis occurs. Once the protein has been synthesized, the mRNA may be degraded and recycled. Post-transcriptional modifications can also occur to mRNA, such as alternative splicing and addition of a 5' cap and a poly(A) tail, which can affect its stability, localization, and translation efficiency.

Molecular sequence data refers to the specific arrangement of molecules, most commonly nucleotides in DNA or RNA, or amino acids in proteins, that make up a biological macromolecule. This data is generated through laboratory techniques such as sequencing, and provides information about the exact order of the constituent molecules. This data is crucial in various fields of biology, including genetics, evolution, and molecular biology, allowing for comparisons between different organisms, identification of genetic variations, and studies of gene function and regulation.

Alternative splicing is a process in molecular biology that occurs during the post-transcriptional modification of pre-messenger RNA (pre-mRNA) molecules. It involves the removal of non-coding sequences, known as introns, and the joining together of coding sequences, or exons, to form a mature messenger RNA (mRNA) molecule that can be translated into a protein.

In alternative splicing, different combinations of exons are selected and joined together to create multiple distinct mRNA transcripts from a single pre-mRNA template. This process increases the diversity of proteins that can be produced from a limited number of genes, allowing for greater functional complexity in organisms.

Alternative splicing is regulated by various cis-acting elements and trans-acting factors that bind to specific sequences in the pre-mRNA molecule and influence which exons are included or excluded during splicing. Abnormal alternative splicing has been implicated in several human diseases, including cancer, neurological disorders, and cardiovascular disease.

RNA precursors, also known as primary transcripts or pre-messenger RNAs (pre-mRNAs), refer to the initial RNA molecules that are synthesized during the transcription process in which DNA is copied into RNA. These precursor molecules still contain non-coding sequences and introns, which need to be removed through a process called splicing, before they can become mature and functional RNAs such as messenger RNAs (mRNAs), ribosomal RNAs (rRNAs), or transfer RNAs (tRNAs).

Pre-mRNAs undergo several processing steps, including 5' capping, 3' polyadenylation, and splicing, to generate mature mRNA molecules that can be translated into proteins. The accurate and efficient production of RNA precursors and their subsequent processing are crucial for gene expression and regulation in cells.

Introns are non-coding sequences of DNA that are present within the genes of eukaryotic organisms, including plants, animals, and humans. Introns are removed during the process of RNA splicing, in which the initial RNA transcript is cut and reconnected to form a mature, functional RNA molecule.

After the intron sequences are removed, the remaining coding sequences, known as exons, are joined together to create a continuous stretch of genetic information that can be translated into a protein or used to produce non-coding RNAs with specific functions. The removal of introns allows for greater flexibility in gene expression and regulation, enabling the generation of multiple proteins from a single gene through alternative splicing.

In summary, introns are non-coding DNA sequences within genes that are removed during RNA processing to create functional RNA molecules or proteins.

Exons are the coding regions of DNA that remain in the mature, processed mRNA after the removal of non-coding intronic sequences during RNA splicing. These exons contain the information necessary to encode proteins, as they specify the sequence of amino acids within a polypeptide chain. The arrangement and order of exons can vary between different genes and even between different versions of the same gene (alternative splicing), allowing for the generation of multiple protein isoforms from a single gene. This complexity in exon structure and usage significantly contributes to the diversity and functionality of the proteome.

RNA (Ribonucleic Acid) is a single-stranded, linear polymer of ribonucleotides. It is a nucleic acid present in the cells of all living organisms and some viruses. RNAs play crucial roles in various biological processes such as protein synthesis, gene regulation, and cellular signaling. There are several types of RNA including messenger RNA (mRNA), ribosomal RNA (rRNA), transfer RNA (tRNA), small nuclear RNA (snRNA), microRNA (miRNA), and long non-coding RNA (lncRNA). These RNAs differ in their structure, function, and location within the cell.

A viral RNA (ribonucleic acid) is the genetic material found in certain types of viruses, as opposed to viruses that contain DNA (deoxyribonucleic acid). These viruses are known as RNA viruses. The RNA can be single-stranded or double-stranded and can exist as several different forms, such as positive-sense, negative-sense, or ambisense RNA. Upon infecting a host cell, the viral RNA uses the host's cellular machinery to translate the genetic information into proteins, leading to the production of new virus particles and the continuation of the viral life cycle. Examples of human diseases caused by RNA viruses include influenza, COVID-19 (SARS-CoV-2), hepatitis C, and polio.

Small nuclear RNA (snRNA) are a type of RNA molecules that are typically around 100-300 nucleotides in length. They are found within the nucleus of eukaryotic cells and are components of small nuclear ribonucleoproteins (snRNPs), which play important roles in various aspects of RNA processing, including splicing of pre-messenger RNA (pre-mRNA) and regulation of transcription.

There are several classes of snRNAs, each with a distinct function. The most well-studied class is the spliceosomal snRNAs, which include U1, U2, U4, U5, and U6 snRNAs. These snRNAs form complexes with proteins to form small nuclear ribonucleoprotein particles (snRNPs) that recognize specific sequences in pre-mRNA and catalyze the removal of introns during splicing.

Other classes of snRNAs include signal recognition particle (SRP) RNA, which is involved in targeting proteins to the endoplasmic reticulum, and Ro60 RNA, which is associated with autoimmune diseases such as systemic lupus erythematosus.

Overall, small nuclear RNAs are essential components of the cellular machinery that regulates gene expression and protein synthesis in eukaryotic cells.

Small interfering RNA (siRNA) is a type of short, double-stranded RNA molecule that plays a role in the RNA interference (RNAi) pathway. The RNAi pathway is a natural cellular process that regulates gene expression by targeting and destroying specific messenger RNA (mRNA) molecules, thereby preventing the translation of those mRNAs into proteins.

SiRNAs are typically 20-25 base pairs in length and are generated from longer double-stranded RNA precursors called hairpin RNAs or dsRNAs by an enzyme called Dicer. Once generated, siRNAs associate with a protein complex called the RNA-induced silencing complex (RISC), which uses one strand of the siRNA (the guide strand) to recognize and bind to complementary sequences in the target mRNA. The RISC then cleaves the target mRNA, leading to its degradation and the inhibition of protein synthesis.

SiRNAs have emerged as a powerful tool for studying gene function and have shown promise as therapeutic agents for a variety of diseases, including viral infections, cancer, and genetic disorders. However, their use as therapeutics is still in the early stages of development, and there are challenges associated with delivering siRNAs to specific cells and tissues in the body.

A spliceosome is a complex of ribonucleoprotein (RNP) particles found in the nucleus of eukaryotic cells that removes introns (non-coding sequences) from precursor messenger RNA (pre-mRNA) and joins exons (coding sequences) together to form mature mRNA. This process is called splicing, which is an essential step in gene expression and protein synthesis. Spliceosomes are composed of five small nuclear ribonucleoprotein particles (snRNPs), known as U1, U2, U4/U6, and U5 snRNPs, and numerous proteins. The assembly of spliceosomes and the splicing reaction are highly regulated and can be influenced by various factors, including cis-acting elements in pre-mRNA and trans-acting factors such as serine/arginine-rich (SR) proteins.

A ribonucleoprotein, U1 small nuclear (U1 snRNP) is a type of small nuclear ribonucleoprotein (snRNP) particle that is found within the nucleus of eukaryotic cells. These complexes are essential for various aspects of RNA processing, particularly in the form of spliceosomes, which are responsible for removing introns from pre-messenger RNA (pre-mRNA) during the process of gene expression.

The U1 snRNP is composed of a small nuclear RNA (snRNA) molecule called U1 snRNA, several proteins, and occasionally other non-coding RNAs. The U1 snRNA contains conserved sequences that recognize and bind to specific sequences in the pre-mRNA, forming base pairs with complementary regions within the intron. This interaction is crucial for the accurate identification and removal of introns during splicing.

In addition to its role in splicing, U1 snRNP has been implicated in other cellular processes such as transcription regulation, RNA decay, and DNA damage response. Dysregulation or mutations in U1 snRNP components have been associated with various human diseases, including cancer and neurological disorders.

RNA editing is a process that alters the sequence of a transcribed RNA molecule after it has been synthesized from DNA, but before it is translated into protein. This can result in changes to the amino acid sequence of the resulting protein or to the regulation of gene expression. The most common type of RNA editing in mammals is the hydrolytic deamination of adenosine (A) to inosine (I), catalyzed by a family of enzymes called adenosine deaminases acting on RNA (ADARs). Inosine is recognized as guanosine (G) by the translation machinery, leading to A-to-G changes in the RNA sequence. Other types of RNA editing include cytidine (C) to uridine (U) deamination and insertion/deletion of nucleotides. RNA editing is a crucial mechanism for generating diversity in gene expression and has been implicated in various biological processes, including development, differentiation, and disease.

A mutation is a permanent change in the DNA sequence of an organism's genome. Mutations can occur spontaneously or be caused by environmental factors such as exposure to radiation, chemicals, or viruses. They may have various effects on the organism, ranging from benign to harmful, depending on where they occur and whether they alter the function of essential proteins. In some cases, mutations can increase an individual's susceptibility to certain diseases or disorders, while in others, they may confer a survival advantage. Mutations are the driving force behind evolution, as they introduce new genetic variability into populations, which can then be acted upon by natural selection.

Ribosomal RNA (rRNA) is a type of RNA molecule that is a key component of ribosomes, which are the cellular structures where protein synthesis occurs in cells. In ribosomes, rRNA plays a crucial role in the process of translation, where genetic information from messenger RNA (mRNA) is translated into proteins.

Ribosomal RNA is synthesized in the nucleus and then transported to the cytoplasm, where it assembles with ribosomal proteins to form ribosomes. Within the ribosome, rRNA provides a structural framework for the assembly of the ribosome and also plays an active role in catalyzing the formation of peptide bonds between amino acids during protein synthesis.

There are several different types of rRNA molecules, including 5S, 5.8S, 18S, and 28S rRNA, which vary in size and function. These rRNA molecules are highly conserved across different species, indicating their essential role in protein synthesis and cellular function.

RNA-binding proteins (RBPs) are a class of proteins that selectively interact with RNA molecules to form ribonucleoprotein complexes. These proteins play crucial roles in the post-transcriptional regulation of gene expression, including pre-mRNA processing, mRNA stability, transport, localization, and translation. RBPs recognize specific RNA sequences or structures through their modular RNA-binding domains, which can be highly degenerate and allow for the recognition of a wide range of RNA targets. The interaction between RBPs and RNA is often dynamic and can be regulated by various post-translational modifications of the proteins or by environmental stimuli, allowing for fine-tuning of gene expression in response to changing cellular needs. Dysregulation of RBP function has been implicated in various human diseases, including neurological disorders and cancer.

Ribonucleic acid (RNA) is a type of nucleic acid that plays a crucial role in the process of gene expression. There are several types of RNA molecules, including messenger RNA (mRNA), ribosomal RNA (rRNA), and transfer RNA (tRNA). These RNA molecules help to transcribe DNA into mRNA, which is then translated into proteins by the ribosomes.

Fungi are a group of eukaryotic organisms that include microorganisms such as yeasts and molds, as well as larger organisms like mushrooms. Like other eukaryotes, fungi contain DNA and RNA as part of their genetic material. The RNA in fungi is similar to the RNA found in other organisms, including humans, and plays a role in gene expression and protein synthesis.

A specific medical definition of "RNA, fungal" does not exist, as RNA is a fundamental component of all living organisms, including fungi. However, RNA can be used as a target for antifungal drugs, as certain enzymes involved in RNA synthesis and processing are unique to fungi and can be inhibited by these drugs. For example, the antifungal drug flucytosine is converted into a toxic metabolite that inhibits fungal RNA and DNA synthesis.

Ribonucleoproteins (RNPs) are complexes composed of ribonucleic acid (RNA) and proteins. They play crucial roles in various cellular processes, including gene expression, RNA processing, transport, stability, and degradation. Different types of RNPs exist, such as ribosomes, spliceosomes, and signal recognition particles, each having specific functions in the cell.

Ribosomes are large RNP complexes responsible for protein synthesis, where messenger RNA (mRNA) is translated into proteins. They consist of two subunits: a smaller subunit containing ribosomal RNA (rRNA) and proteins that recognize the start codon on mRNA, and a larger subunit with rRNA and proteins that facilitate peptide bond formation during translation.

Spliceosomes are dynamic RNP complexes involved in pre-messenger RNA (pre-mRNA) splicing, where introns (non-coding sequences) are removed, and exons (coding sequences) are joined together to form mature mRNA. Spliceosomes consist of five small nuclear ribonucleoproteins (snRNPs), each containing a specific small nuclear RNA (snRNA) and several proteins, as well as numerous additional proteins.

Other RNP complexes include signal recognition particles (SRPs), which are responsible for targeting secretory and membrane proteins to the endoplasmic reticulum during translation, and telomerase, an enzyme that maintains the length of telomeres (the protective ends of chromosomes) by adding repetitive DNA sequences using its built-in RNA component.

In summary, ribonucleoproteins are essential complexes in the cell that participate in various aspects of RNA metabolism and protein synthesis.

Bacterial RNA refers to the genetic material present in bacteria that is composed of ribonucleic acid (RNA). Unlike higher organisms, bacteria contain a single circular chromosome made up of DNA, along with smaller circular pieces of DNA called plasmids. These bacterial genetic materials contain the information necessary for the growth and reproduction of the organism.

Bacterial RNA can be divided into three main categories: messenger RNA (mRNA), ribosomal RNA (rRNA), and transfer RNA (tRNA). mRNA carries genetic information copied from DNA, which is then translated into proteins by the rRNA and tRNA molecules. rRNA is a structural component of the ribosome, where protein synthesis occurs, while tRNA acts as an adapter that brings amino acids to the ribosome during protein synthesis.

Bacterial RNA plays a crucial role in various cellular processes, including gene expression, protein synthesis, and regulation of metabolic pathways. Understanding the structure and function of bacterial RNA is essential for developing new antibiotics and other therapeutic strategies to combat bacterial infections.

HeLa cells are a type of immortalized cell line used in scientific research. They are derived from a cancer that developed in the cervical tissue of Henrietta Lacks, an African-American woman, in 1951. After her death, cells taken from her tumor were found to be capable of continuous division and growth in a laboratory setting, making them an invaluable resource for medical research.

HeLa cells have been used in a wide range of scientific studies, including research on cancer, viruses, genetics, and drug development. They were the first human cell line to be successfully cloned and are able to grow rapidly in culture, doubling their population every 20-24 hours. This has made them an essential tool for many areas of biomedical research.

It is important to note that while HeLa cells have been instrumental in numerous scientific breakthroughs, the story of their origin raises ethical questions about informed consent and the use of human tissue in research.

Small nuclear ribonucleoproteins (snRNPs) are a type of ribonucleoprotein (RNP) found within the nucleus of eukaryotic cells. They are composed of small nuclear RNA (snRNA) molecules and associated proteins, which are involved in various aspects of RNA processing, particularly in the modification and splicing of messenger RNA (mRNA).

The snRNPs play a crucial role in the formation of spliceosomes, large ribonucleoprotein complexes that remove introns (non-coding sequences) from pre-mRNA and join exons (coding sequences) together to form mature mRNA. Each snRNP contains a specific snRNA molecule, such as U1, U2, U4, U5, or U6, which recognizes and binds to specific sequences within the pre-mRNA during splicing. The associated proteins help stabilize the snRNP structure and facilitate its interactions with other components of the spliceosome.

In addition to their role in splicing, some snRNPs are also involved in other cellular processes, such as transcription regulation, RNA export, and DNA damage response. Dysregulation or mutations in snRNP components have been implicated in various human diseases, including cancer, neurological disorders, and autoimmune diseases.

Nucleic acid conformation refers to the three-dimensional structure that nucleic acids (DNA and RNA) adopt as a result of the bonding patterns between the atoms within the molecule. The primary structure of nucleic acids is determined by the sequence of nucleotides, while the conformation is influenced by factors such as the sugar-phosphate backbone, base stacking, and hydrogen bonding.

Two common conformations of DNA are the B-form and the A-form. The B-form is a right-handed helix with a diameter of about 20 Å and a pitch of 34 Å, while the A-form has a smaller diameter (about 18 Å) and a shorter pitch (about 25 Å). RNA typically adopts an A-form conformation.

The conformation of nucleic acids can have significant implications for their function, as it can affect their ability to interact with other molecules such as proteins or drugs. Understanding the conformational properties of nucleic acids is therefore an important area of research in molecular biology and medicine.

A catalytic RNA, often referred to as a ribozyme, is a type of RNA molecule that has the ability to act as an enzyme and catalyze chemical reactions. These RNA molecules contain specific sequences and structures that allow them to bind to other molecules and accelerate chemical reactions without being consumed in the process.

Ribozymes play important roles in various biological processes, such as RNA splicing, translation regulation, and gene expression. One of the most well-known ribozymes is the self-splicing intron found in certain RNA molecules, which can excise itself from the host RNA and then ligase the flanking exons together.

The discovery of catalytic RNAs challenged the central dogma of molecular biology, which held that proteins were solely responsible for carrying out biological catalysis. The finding that RNA could also function as an enzyme opened up new avenues of research and expanded our understanding of the complexity and versatility of biological systems.

A ribonucleoprotein, U5 small nuclear (snRNP), is a type of spliceosomal small nuclear ribonucleoprotein (snRNP) particle that plays a crucial role in the process of pre-messenger RNA (pre-mRNA) splicing. Pre-mRNA splicing is the removal of non-coding sequences, called introns, from the pre-mRNA molecule and the joining together of the remaining coding sequences, or exons, to form a mature mRNA molecule that can be translated into protein.

The U5 snRNP particle consists of a small uridine-rich RNA (U5 snRNA) molecule and several associated proteins. The U5 snRNA contains highly conserved sequences that are important for its recognition by the other components of the spliceosome, which is the large ribonucleoprotein complex responsible for pre-mRNA splicing.

During the splicing process, the U5 snRNP particle interacts with other snRNP particles (U1, U2, and U4/U6) to form a functional spliceosome that catalyzes the splicing reaction. The U5 snRNA base-pairs with the intron sequences at the 5' and 3' splice sites, helping to position the exons for splicing. After the splicing reaction is complete, the U5 snRNP particle is released from the spliceosome and can be recycled for further rounds of splicing.

Defects in the components of the U5 snRNP particle have been implicated in several human diseases, including certain forms of cancer and neurological disorders.

An amino acid sequence is the specific order of amino acids in a protein or peptide molecule, formed by the linking of the amino group (-NH2) of one amino acid to the carboxyl group (-COOH) of another amino acid through a peptide bond. The sequence is determined by the genetic code and is unique to each type of protein or peptide. It plays a crucial role in determining the three-dimensional structure and function of proteins.

RNA interference (RNAi) is a biological process in which RNA molecules inhibit the expression of specific genes. This process is mediated by small RNA molecules, including microRNAs (miRNAs) and small interfering RNAs (siRNAs), that bind to complementary sequences on messenger RNA (mRNA) molecules, leading to their degradation or translation inhibition.

RNAi plays a crucial role in regulating gene expression and defending against foreign genetic elements, such as viruses and transposons. It has also emerged as an important tool for studying gene function and developing therapeutic strategies for various diseases, including cancer and viral infections.

DNA-directed RNA polymerases are enzymes that synthesize RNA molecules using a DNA template in a process called transcription. These enzymes read the sequence of nucleotides in a DNA molecule and use it as a blueprint to construct a complementary RNA strand.

The RNA polymerase moves along the DNA template, adding ribonucleotides one by one to the growing RNA chain. The synthesis is directional, starting at the promoter region of the DNA and moving towards the terminator region.

In bacteria, there is a single type of RNA polymerase that is responsible for transcribing all types of RNA (mRNA, tRNA, and rRNA). In eukaryotic cells, however, there are three different types of RNA polymerases: RNA polymerase I, II, and III. Each type is responsible for transcribing specific types of RNA.

RNA polymerases play a crucial role in gene expression, as they link the genetic information encoded in DNA to the production of functional proteins. Inhibition or mutation of these enzymes can have significant consequences for cellular function and survival.

A ribonucleoprotein, U2 small nuclear (U2 snRNP) is a type of spliceosomal small nuclear ribonucleoprotein (snRNP) complex that plays a crucial role in the pre-messenger RNA (pre-mRNA) splicing process during gene expression in eukaryotic cells.

Pre-mRNA splicing is the removal of non-coding sequences, called introns, from the pre-mRNA molecule and the joining together of the remaining coding sequences, or exons, to form a continuous mRNA sequence that can be translated into protein. U2 snRNPs are essential components of the spliceosome, the large ribonucleoprotein complex responsible for pre-mRNA splicing.

The U2 snRNP is composed of several proteins and a small nuclear RNA (snRNA) molecule called U2 small nuclear RNA (U2 snRNA). The U2 snRNA binds to specific sequences within the pre-mRNA, forming part of the intron's branch site, which helps define the boundaries of the exons and introns. This interaction facilitates the recognition and assembly of other spliceosomal components, ultimately leading to the precise excision of introns and ligation of exons in the mature mRNA molecule.

In summary, U2 snRNP is a ribonucleoprotein complex involved in pre-mRNA splicing, where it plays a critical role in recognizing and processing intron-exon boundaries during gene expression in eukaryotic cells.

Post-transcriptional RNA processing refers to the modifications and regulations that occur on RNA molecules after the transcription of DNA into RNA. This process includes several steps:

1. 5' capping: The addition of a cap structure, usually a methylated guanosine triphosphate (GTP), to the 5' end of the RNA molecule. This helps protect the RNA from degradation and plays a role in its transport, stability, and translation.
2. 3' polyadenylation: The addition of a string of adenosine residues (poly(A) tail) to the 3' end of the RNA molecule. This process is important for mRNA stability, export from the nucleus, and translation initiation.
3. Intron removal and exon ligation: Eukaryotic pre-messenger RNAs (pre-mRNAs) contain intronic sequences that do not code for proteins. These introns are removed by a process called splicing, where the flanking exons are joined together to form a continuous mRNA sequence. Alternative splicing can lead to different mature mRNAs from a single pre-mRNA, increasing transcriptomic and proteomic diversity.
4. RNA editing: Specific nucleotide changes in RNA molecules that alter the coding potential or regulatory functions of RNA. This process is catalyzed by enzymes like ADAR (Adenosine Deaminases Acting on RNA) and APOBEC (Apolipoprotein B mRNA Editing Catalytic Polypeptide-like).
5. Chemical modifications: Various chemical modifications can occur on RNA nucleotides, such as methylation, pseudouridination, and isomerization. These modifications can influence RNA stability, localization, and interaction with proteins or other RNAs.
6. Transport and localization: Mature mRNAs are transported from the nucleus to the cytoplasm for translation. In some cases, specific mRNAs are localized to particular cellular compartments to ensure local protein synthesis.
7. Degradation: RNA molecules have finite lifetimes and undergo degradation by various ribonucleases (RNases). The rate of degradation can be influenced by factors such as RNA structure, modifications, or interactions with proteins.

RNA viruses are a type of virus that contain ribonucleic acid (RNA) as their genetic material, as opposed to deoxyribonucleic acid (DNA). RNA viruses replicate by using an enzyme called RNA-dependent RNA polymerase to transcribe and replicate their RNA genome.

There are several different groups of RNA viruses, including:

1. Negative-sense single-stranded RNA viruses: These viruses have a genome that is complementary to the mRNA and must undergo transcription to produce mRNA before translation can occur. Examples include influenza virus, measles virus, and rabies virus.
2. Positive-sense single-stranded RNA viruses: These viruses have a genome that can serve as mRNA and can be directly translated into protein after entry into the host cell. Examples include poliovirus, rhinoviruses, and coronaviruses.
3. Double-stranded RNA viruses: These viruses have a genome consisting of double-stranded RNA and use a complex replication strategy involving both transcription and reverse transcription. Examples include rotaviruses and reoviruses.

RNA viruses are known to cause a wide range of human diseases, ranging from the common cold to more severe illnesses such as hepatitis C, polio, and COVID-19. Due to their high mutation rates and ability to adapt quickly to new environments, RNA viruses can be difficult to control and treat with antiviral drugs or vaccines.

Protein isoforms are different forms or variants of a protein that are produced from a single gene through the process of alternative splicing, where different exons (or parts of exons) are included in the mature mRNA molecule. This results in the production of multiple, slightly different proteins that share a common core structure but have distinct sequences and functions. Protein isoforms can also arise from genetic variations such as single nucleotide polymorphisms or mutations that alter the protein-coding sequence of a gene. These differences in protein sequence can affect the stability, localization, activity, or interaction partners of the protein isoform, leading to functional diversity and specialization within cells and organisms.

I'm happy to help! However, it seems there might be a slight misunderstanding in your question. RNA, or ribonucleic acid, is typically single-stranded. Unlike DNA, which is double-stranded and forms a double helix, RNA usually exists as a single strand of nucleotides.

There are exceptions to this rule, such as certain types of RNA molecules that can form double-stranded structures in specific contexts. For example:

1. Double-Stranded RNA (dsRNA) viruses: These viruses have genomes made entirely of RNA, which is double-stranded throughout or partially double-stranded. The dsRNA viruses include important pathogens such as rotaviruses and reoviruses.
2. Hairpin loops in RNA structures: Some single-stranded RNA molecules can fold back on themselves to form short double-stranded regions, called hairpin loops, within their overall structure. These are often found in ribosomal RNA (rRNA), transfer RNA (tRNA), and messenger RNA (mRNA) molecules.

So, while 'double-stranded RNA' is not a standard medical definition for RNA itself, there are specific instances where RNA can form double-stranded structures as described above.

DNA Mutational Analysis is a laboratory test used to identify genetic variations or changes (mutations) in the DNA sequence of a gene. This type of analysis can be used to diagnose genetic disorders, predict the risk of developing certain diseases, determine the most effective treatment for cancer, or assess the likelihood of passing on an inherited condition to offspring.

The test involves extracting DNA from a patient's sample (such as blood, saliva, or tissue), amplifying specific regions of interest using polymerase chain reaction (PCR), and then sequencing those regions to determine the precise order of nucleotide bases in the DNA molecule. The resulting sequence is then compared to reference sequences to identify any variations or mutations that may be present.

DNA Mutational Analysis can detect a wide range of genetic changes, including single-nucleotide polymorphisms (SNPs), insertions, deletions, duplications, and rearrangements. The test is often used in conjunction with other diagnostic tests and clinical evaluations to provide a comprehensive assessment of a patient's genetic profile.

It is important to note that not all mutations are pathogenic or associated with disease, and the interpretation of DNA Mutational Analysis results requires careful consideration of the patient's medical history, family history, and other relevant factors.

Nucleic acid precursors are the molecules that are used in the synthesis of nucleotides, which are the building blocks of nucleic acids, including DNA and RNA. The two main types of nucleic acid precursors are nucleoside triphosphates (deoxyribonucleoside triphosphates for DNA and ribonucleoside triphosphates for RNA) and their corresponding pentose sugars (deoxyribose for DNA and ribose for RNA).

Nucleoside triphosphates consist of a nitrogenous base, a pentose sugar, and three phosphate groups. The nitrogenous bases in nucleic acids are classified as purines (adenine and guanine) or pyrimidines (thymine, cytosine, and uracil). In the synthesis of nucleotides, nucleophilic attack by the nitrogenous base on a pentose sugar in the form of a phosphate ester leads to the formation of a glycosidic bond between the base and the sugar. The addition of two more phosphate groups through anhydride linkages forms the nucleoside triphosphate.

The synthesis of nucleic acids involves the sequential addition of nucleotides to a growing chain, with the removal of a pyrophosphate group from each nucleotide providing energy for the reaction. The process is catalyzed by enzymes called polymerases, which use nucleic acid templates to ensure the correct base-pairing and sequence of nucleotides in the final product.

In summary, nucleic acid precursors are the molecules that provide the building blocks for the synthesis of DNA and RNA, and include nucleoside triphosphates and their corresponding pentose sugars.

Heterogeneous Nuclear Ribonucleoproteins (hnRNPs) are a group of nuclear proteins that are involved in the processing and metabolism of messenger RNA (mRNA). They were named "heterogeneous" because they were initially found to be associated with a heterogeneous population of RNA molecules. The hnRNPs are divided into several subfamilies, A and B being two of them.

The hnRNP A-B group is composed of proteins that share structural similarities and have overlapping functions in the regulation of mRNA metabolism. These proteins play a role in various aspects of RNA processing, including splicing, 3' end processing, transport, stability, and translation.

The hnRNP A-B group includes several members, such as hnRNPA1, hnRNPA2/B1, and hnRNPC. These proteins contain RNA recognition motifs (RRMs) that allow them to bind to specific sequences in the RNA molecules. They can also interact with other proteins and form complexes that regulate mRNA function.

Mutations in genes encoding hnRNP A-B group members have been associated with several human diseases, including neurodegenerative disorders, myopathies, and cancer. Therefore, understanding the structure and function of these proteins is essential for elucidating their role in disease pathogenesis and developing potential therapeutic strategies.

RNA helicases are a class of enzymes that are capable of unwinding RNA secondary structures using the energy derived from ATP hydrolysis. They play crucial roles in various cellular processes involving RNA, such as transcription, splicing, translation, ribosome biogenesis, and RNA degradation. RNA helicases can be divided into several superfamilies based on their sequence and structural similarities, with the two largest being superfamily 1 (SF1) and superfamily 2 (SF2). These enzymes typically contain conserved motifs that are involved in ATP binding and hydrolysis, as well as RNA binding. By unwinding RNA structures, RNA helicases facilitate the access of other proteins to their target RNAs, thereby enabling the coordinated regulation of RNA metabolism.

RNA Sequence Analysis is a branch of bioinformatics that involves the determination and analysis of the nucleotide sequence of Ribonucleic Acid (RNA) molecules. This process includes identifying and characterizing the individual RNA molecules, determining their functions, and studying their evolutionary relationships.

RNA Sequence Analysis typically involves the use of high-throughput sequencing technologies to generate large datasets of RNA sequences, which are then analyzed using computational methods. The analysis may include comparing the sequences to reference databases to identify known RNA molecules or discovering new ones, identifying patterns and features in the sequences, such as motifs or domains, and predicting the secondary and tertiary structures of the RNA molecules.

RNA Sequence Analysis has many applications in basic research, including understanding gene regulation, identifying novel non-coding RNAs, and studying evolutionary relationships between organisms. It also has practical applications in clinical settings, such as diagnosing and monitoring diseases, developing new therapies, and personalized medicine.

Genetic transcription is the process by which the information in a strand of DNA is used to create a complementary RNA molecule. This process is the first step in gene expression, where the genetic code in DNA is converted into a form that can be used to produce proteins or functional RNAs.

During transcription, an enzyme called RNA polymerase binds to the DNA template strand and reads the sequence of nucleotide bases. As it moves along the template, it adds complementary RNA nucleotides to the growing RNA chain, creating a single-stranded RNA molecule that is complementary to the DNA template strand. Once transcription is complete, the RNA molecule may undergo further processing before it can be translated into protein or perform its functional role in the cell.

Transcription can be either "constitutive" or "regulated." Constitutive transcription occurs at a relatively constant rate and produces essential proteins that are required for basic cellular functions. Regulated transcription, on the other hand, is subject to control by various intracellular and extracellular signals, allowing cells to respond to changing environmental conditions or developmental cues.

Heterogeneous Nuclear Ribonucleoproteins (hnRNPs) are a group of nuclear proteins that are involved in the processing and metabolism of messenger RNA (mRNA). The hnRNPs are divided into several subgroups, A to U.

The F/H subgroup includes two closely related proteins, hnRNP F and hnRNP H, which share a high degree of sequence similarity. These proteins are involved in various aspects of mRNA metabolism, including splicing, 3'-end processing, transport, stability, and translation.

Specifically, hnRNP F has been shown to play a role in the regulation of alternative splicing by binding to specific RNA sequences and modulating splice site selection. It also interacts with other proteins involved in splicing and mRNA transport.

Similarly, hnRNP H is involved in various aspects of mRNA metabolism, including splicing, 3'-end processing, and translation. It has been shown to bind to specific RNA sequences and regulate alternative splicing by promoting or repressing the inclusion of certain exons.

Together, hnRNP F and hnRNP H form heterodimers that can interact with other proteins and RNAs to regulate gene expression in a coordinated manner. Mutations in these proteins have been associated with various human diseases, including cancer and neurological disorders.

A ribonucleoprotein, U4-U6 small nuclear (snRNP) is a type of small nuclear ribonucleoprotein particle that plays a crucial role in the splicing of pre-messenger RNA (pre-mRNA) in the nucleus of eukaryotic cells. Specifically, U4-U6 snRNP is part of the spliceosome complex, which catalyzes the removal of introns (non-coding sequences) from pre-mRNA during the process of gene expression.

The U4-U6 snRNP is composed of several proteins and three small nuclear RNAs (snRNAs): U4, U6, and U6atac. These snRNAs are highly conserved across different species and are essential for the stability and function of the U4-U6 snRNP complex. The U4 and U6 snRNAs form a specific base-pairing interaction that is critical for the assembly and activity of the spliceosome.

During splicing, the U4-U6 snRNP interacts with other snRNPs (U1, U2, and U5) to form a large ribonucleoprotein complex called the spliceosome. The U4-U6 snRNP then undergoes a series of conformational changes that ultimately lead to the formation of the active site for splicing. This process involves the displacement of U4 snRNA from U6 snRNA, allowing U6 snRNA to base-pair with the intron and form the catalytic core of the spliceosome.

Defects in U4-U6 snRNP biogenesis or function have been implicated in various human diseases, including cancer, neurological disorders, and autoimmune diseases.

RNA stability refers to the duration that a ribonucleic acid (RNA) molecule remains intact and functional within a cell before it is degraded or broken down into its component nucleotides. Various factors can influence RNA stability, including:

1. Primary sequence: Certain sequences in the RNA molecule may be more susceptible to degradation by ribonucleases (RNases), enzymes that break down RNA.
2. Secondary structure: The formation of stable secondary structures, such as hairpins or stem-loop structures, can protect RNA from degradation.
3. Presence of RNA-binding proteins: Proteins that bind to RNA can either stabilize or destabilize the RNA molecule, depending on the type and location of the protein-RNA interaction.
4. Chemical modifications: Modifications to the RNA nucleotides, such as methylation, can increase RNA stability by preventing degradation.
5. Subcellular localization: The subcellular location of an RNA molecule can affect its stability, with some locations providing more protection from ribonucleases than others.
6. Cellular conditions: Changes in cellular conditions, such as pH or temperature, can also impact RNA stability.

Understanding RNA stability is important for understanding gene regulation and the function of non-coding RNAs, as well as for developing RNA-based therapeutic strategies.

RNA Polymerase II is a type of enzyme responsible for transcribing DNA into RNA in eukaryotic cells. It plays a crucial role in the process of gene expression, where the information stored in DNA is used to create proteins. Specifically, RNA Polymerase II transcribes protein-coding genes to produce precursor messenger RNA (pre-mRNA), which is then processed into mature mRNA. This mature mRNA serves as a template for protein synthesis during translation.

RNA Polymerase II has a complex structure, consisting of multiple subunits, and it requires the assistance of various transcription factors and coactivators to initiate and regulate transcription. The enzyme recognizes specific promoter sequences in DNA, unwinds the double-stranded DNA, and synthesizes a complementary RNA strand using one of the unwound DNA strands as a template. This process results in the formation of a nascent RNA molecule that is further processed into mature mRNA for protein synthesis or other functional RNAs involved in gene regulation.

Antisense RNA is a type of RNA molecule that is complementary to another RNA called sense RNA. In the context of gene expression, sense RNA is the RNA transcribed from a protein-coding gene, which serves as a template for translation into a protein. Antisense RNA, on the other hand, is transcribed from the opposite strand of the DNA and is complementary to the sense RNA.

Antisense RNA can bind to its complementary sense RNA through base-pairing, forming a double-stranded RNA structure. This interaction can prevent the sense RNA from being translated into protein or can target it for degradation by cellular machinery, thereby reducing the amount of protein produced from the gene. Antisense RNA can be used as a tool in molecular biology to study gene function or as a therapeutic strategy to silence disease-causing genes.

A point mutation is a type of genetic mutation where a single nucleotide base (A, T, C, or G) in DNA is altered, deleted, or substituted with another nucleotide. Point mutations can have various effects on the organism, depending on the location of the mutation and whether it affects the function of any genes. Some point mutations may not have any noticeable effect, while others might lead to changes in the amino acids that make up proteins, potentially causing diseases or altering traits. Point mutations can occur spontaneously due to errors during DNA replication or be inherited from parents.

Polymerase Chain Reaction (PCR) is a laboratory technique used to amplify specific regions of DNA. It enables the production of thousands to millions of copies of a particular DNA sequence in a rapid and efficient manner, making it an essential tool in various fields such as molecular biology, medical diagnostics, forensic science, and research.

The PCR process involves repeated cycles of heating and cooling to separate the DNA strands, allow primers (short sequences of single-stranded DNA) to attach to the target regions, and extend these primers using an enzyme called Taq polymerase, resulting in the exponential amplification of the desired DNA segment.

In a medical context, PCR is often used for detecting and quantifying specific pathogens (viruses, bacteria, fungi, or parasites) in clinical samples, identifying genetic mutations or polymorphisms associated with diseases, monitoring disease progression, and evaluating treatment effectiveness.

Heterogeneous Nuclear Ribonucleoproteins (hnRNPs) are a type of nuclear protein complex associated with nascent RNA transcripts in the nucleus of eukaryotic cells. They play crucial roles in various aspects of RNA metabolism, including processing, transport, stability, and translation.

The term "heterogeneous" refers to the diverse range of proteins that make up these complexes, while "nuclear" indicates their location within the nucleus. The hnRNPs are composed of a core protein component and associated RNA molecules, primarily heterogeneous nuclear RNAs (hnRNAs) or pre-messenger RNAs (pre-mRNAs).

There are over 20 different hnRNP proteins identified so far, each with distinct functions and structures. Some of the well-known hnRNPs include hnRNP A1, hnRNP C, and hnRNP U. These proteins contain several domains that facilitate RNA binding, protein-protein interactions, and post-translational modifications.

The primary function of hnRNPs is to regulate gene expression at the post-transcriptional level by interacting with RNA molecules. They participate in splicing, 3' end processing, export, localization, stability, and translation of mRNAs. Dysregulation of hnRNP function has been implicated in various human diseases, including neurological disorders and cancer.

RNA folding, also known as RNA structure formation or RNA tertiary structure prediction, refers to the process by which an RNA molecule folds into a specific three-dimensional shape based on its primary sequence. This shape is determined by intramolecular interactions between nucleotides within the RNA chain, including base pairing (through hydrogen bonding) and stacking interactions. The folded structure of RNA plays a crucial role in its function, as it can create specific binding sites for proteins or other molecules, facilitate or inhibit enzymatic activity, or influence the stability and localization of the RNA within the cell.

RNA folding is a complex process that can be influenced by various factors such as temperature, ionic conditions, and molecular crowding. The folded structure of an RNA molecule can be predicted using computational methods, such as thermodynamic modeling and machine learning algorithms, which take into account the primary sequence and known patterns of base pairing and stacking interactions to generate a model of the three-dimensional structure. However, experimental techniques, such as chemical probing and crystallography, are often necessary to validate and refine these predictions.

Nuclear proteins are a category of proteins that are primarily found in the nucleus of a eukaryotic cell. They play crucial roles in various nuclear functions, such as DNA replication, transcription, repair, and RNA processing. This group includes structural proteins like lamins, which form the nuclear lamina, and regulatory proteins, such as histones and transcription factors, that are involved in gene expression. Nuclear localization signals (NLS) often help target these proteins to the nucleus by interacting with importin proteins during active transport across the nuclear membrane.

A cell line is a culture of cells that are grown in a laboratory for use in research. These cells are usually taken from a single cell or group of cells, and they are able to divide and grow continuously in the lab. Cell lines can come from many different sources, including animals, plants, and humans. They are often used in scientific research to study cellular processes, disease mechanisms, and to test new drugs or treatments. Some common types of human cell lines include HeLa cells (which come from a cancer patient named Henrietta Lacks), HEK293 cells (which come from embryonic kidney cells), and HUVEC cells (which come from umbilical vein endothelial cells). It is important to note that cell lines are not the same as primary cells, which are cells that are taken directly from a living organism and have not been grown in the lab.

In the context of medical and biological sciences, a "binding site" refers to a specific location on a protein, molecule, or cell where another molecule can attach or bind. This binding interaction can lead to various functional changes in the original protein or molecule. The other molecule that binds to the binding site is often referred to as a ligand, which can be a small molecule, ion, or even another protein.

The binding between a ligand and its target binding site can be specific and selective, meaning that only certain ligands can bind to particular binding sites with high affinity. This specificity plays a crucial role in various biological processes, such as signal transduction, enzyme catalysis, or drug action.

In the case of drug development, understanding the location and properties of binding sites on target proteins is essential for designing drugs that can selectively bind to these sites and modulate protein function. This knowledge can help create more effective and safer therapeutic options for various diseases.

RNA caps are structures found at the 5' end of RNA molecules, including messenger RNA (mRNA), ribosomal RNA (rRNA), and transfer RNA (tRNA). These caps consist of a modified guanine nucleotide (called 7-methylguanosine) that is linked to the first nucleotide of the RNA chain through a triphosphate bridge. The RNA cap plays several important roles in regulating RNA metabolism, including protecting the RNA from degradation by exonucleases, promoting the recognition and binding of the RNA by ribosomes during translation, and modulating the stability and transport of the RNA within the cell.

Ribonucleic acid (RNA) in plants refers to the long, single-stranded molecules that are essential for the translation of genetic information from deoxyribonucleic acid (DNA) into proteins. RNA is a nucleic acid, like DNA, and it is composed of a ribose sugar backbone with attached nitrogenous bases (adenine, uracil, guanine, and cytosine).

In plants, there are several types of RNA that play specific roles in the gene expression process:

1. Messenger RNA (mRNA): This type of RNA carries genetic information copied from DNA in the form of a sequence of three-base code units called codons. These codons specify the order of amino acids in a protein.
2. Transfer RNA (tRNA): tRNAs are small RNA molecules that serve as adaptors between the mRNA and the amino acids during protein synthesis. Each tRNA has a specific anticodon sequence that base-pairs with a complementary codon on the mRNA, and it carries a specific amino acid that corresponds to that codon.
3. Ribosomal RNA (rRNA): rRNAs are structural components of ribosomes, which are large macromolecular complexes where protein synthesis occurs. In plants, there are several types of rRNAs, including the 18S, 5.8S, and 25S/28S rRNAs, that form the core of the ribosome and help catalyze peptide bond formation during protein synthesis.
4. Small nuclear RNA (snRNA): These are small RNA molecules that play a role in RNA processing, such as splicing, where introns (non-coding sequences) are removed from pre-mRNA and exons (coding sequences) are joined together to form mature mRNAs.
5. MicroRNA (miRNA): These are small non-coding RNAs that regulate gene expression by binding to complementary sequences in target mRNAs, leading to their degradation or translation inhibition.

Overall, these different types of RNAs play crucial roles in various aspects of RNA metabolism, gene regulation, and protein synthesis in plants.

Genetic models are theoretical frameworks used in genetics to describe and explain the inheritance patterns and genetic architecture of traits, diseases, or phenomena. These models are based on mathematical equations and statistical methods that incorporate information about gene frequencies, modes of inheritance, and the effects of environmental factors. They can be used to predict the probability of certain genetic outcomes, to understand the genetic basis of complex traits, and to inform medical management and treatment decisions.

There are several types of genetic models, including:

1. Mendelian models: These models describe the inheritance patterns of simple genetic traits that follow Mendel's laws of segregation and independent assortment. Examples include autosomal dominant, autosomal recessive, and X-linked inheritance.
2. Complex trait models: These models describe the inheritance patterns of complex traits that are influenced by multiple genes and environmental factors. Examples include heart disease, diabetes, and cancer.
3. Population genetics models: These models describe the distribution and frequency of genetic variants within populations over time. They can be used to study evolutionary processes, such as natural selection and genetic drift.
4. Quantitative genetics models: These models describe the relationship between genetic variation and phenotypic variation in continuous traits, such as height or IQ. They can be used to estimate heritability and to identify quantitative trait loci (QTLs) that contribute to trait variation.
5. Statistical genetics models: These models use statistical methods to analyze genetic data and infer the presence of genetic associations or linkage. They can be used to identify genetic risk factors for diseases or traits.

Overall, genetic models are essential tools in genetics research and medical genetics, as they allow researchers to make predictions about genetic outcomes, test hypotheses about the genetic basis of traits and diseases, and develop strategies for prevention, diagnosis, and treatment.

Transfer RNA (tRNA) is a type of RNA molecule that plays a crucial role in protein synthesis, the process by which cells create proteins. In protein synthesis, tRNAs serve as adaptors, translating the genetic code present in messenger RNA (mRNA) into the corresponding amino acids required to build a protein.

Each tRNA molecule has a distinct structure, consisting of approximately 70-90 nucleotides arranged in a cloverleaf shape with several loops and stems. The most important feature of a tRNA is its anticodon, a sequence of three nucleotides located in one of the loops. This anticodon base-pairs with a complementary codon on the mRNA during translation, ensuring that the correct amino acid is added to the growing polypeptide chain.

Before tRNAs can participate in protein synthesis, they must be charged with their specific amino acids through an enzymatic process involving aminoacyl-tRNA synthetases. These enzymes recognize and bind to both the tRNA and its corresponding amino acid, forming a covalent bond between them. Once charged, the aminoacyl-tRNA complex is ready to engage in translation and contribute to protein formation.

In summary, transfer RNA (tRNA) is a small RNA molecule that facilitates protein synthesis by translating genetic information from messenger RNA into specific amino acids, ultimately leading to the creation of functional proteins within cells.

I'd be happy to help! However, I believe there might be a slight confusion in your question. RNA stands for Ribonucleic Acid, which is a type of nucleic acid involved in various biological roles in the coding, decoding, regulation, and expression of genes. On the other hand, protozoan refers to a unicellular organism from the kingdom Protista, which includes a wide variety of simple eukaryotic organisms such as amoebas, paramecia, and plasmodium (the malaria-causing parasite).

There isn't a specific medical definition for "RNA, protozoan" since RNA is a molecule present in all living cells, including human cells, and protozoans are a group of organisms. However, I can tell you that RNA plays crucial roles in protozoan biology, such as acting as a messenger between DNA and ribosomes during protein synthesis or regulating gene expression.

If you have any further questions or need more specific information about RNA in protozoans, please let me know!

Complementary DNA (cDNA) is a type of DNA that is synthesized from a single-stranded RNA molecule through the process of reverse transcription. In this process, the enzyme reverse transcriptase uses an RNA molecule as a template to synthesize a complementary DNA strand. The resulting cDNA is therefore complementary to the original RNA molecule and is a copy of its coding sequence, but it does not contain non-coding regions such as introns that are present in genomic DNA.

Complementary DNA is often used in molecular biology research to study gene expression, protein function, and other genetic phenomena. For example, cDNA can be used to create cDNA libraries, which are collections of cloned cDNA fragments that represent the expressed genes in a particular cell type or tissue. These libraries can then be screened for specific genes or gene products of interest. Additionally, cDNA can be used to produce recombinant proteins in heterologous expression systems, allowing researchers to study the structure and function of proteins that may be difficult to express or purify from their native sources.

DNA primers are short single-stranded DNA molecules that serve as a starting point for DNA synthesis. They are typically used in laboratory techniques such as the polymerase chain reaction (PCR) and DNA sequencing. The primer binds to a complementary sequence on the DNA template through base pairing, providing a free 3'-hydroxyl group for the DNA polymerase enzyme to add nucleotides and synthesize a new strand of DNA. This allows for specific and targeted amplification or analysis of a particular region of interest within a larger DNA molecule.

Sequence homology in nucleic acids refers to the similarity or identity between the nucleotide sequences of two or more DNA or RNA molecules. It is often used as a measure of biological relationship between genes, organisms, or populations. High sequence homology suggests a recent common ancestry or functional constraint, while low sequence homology may indicate a more distant relationship or different functions.

Nucleic acid sequence homology can be determined by various methods such as pairwise alignment, multiple sequence alignment, and statistical analysis. The degree of homology is typically expressed as a percentage of identical or similar nucleotides in a given window of comparison.

It's important to note that the interpretation of sequence homology depends on the biological context and the evolutionary distance between the sequences compared. Therefore, functional and experimental validation is often necessary to confirm the significance of sequence homology.

A consensus sequence in genetics refers to the most common nucleotide (DNA or RNA) or amino acid at each position in a multiple sequence alignment. It is derived by comparing and analyzing several sequences of the same gene or protein from different individuals or organisms. The consensus sequence provides a general pattern or motif that is shared among these sequences and can be useful in identifying functional regions, conserved domains, or evolutionary relationships. However, it's important to note that not every sequence will exactly match the consensus sequence, as variations can occur naturally due to mutations or genetic differences among individuals.

DEAD-box RNA helicases are a family of proteins that are involved in unwinding RNA secondary structures and displacing proteins bound to RNA molecules. They get their name from the conserved amino acid sequence motif "DEAD" (Asp-Glu-Ala-Asp) found within their catalytic core, which is responsible for ATP-dependent helicase activity. These enzymes play crucial roles in various aspects of RNA metabolism, including pre-mRNA splicing, ribosome biogenesis, translation initiation, and RNA decay. DEAD-box helicases are also implicated in a number of human diseases, such as cancer and neurological disorders.

I must clarify that the term "pedigree" is not typically used in medical definitions. Instead, it is often employed in genetics and breeding, where it refers to the recorded ancestry of an individual or a family, tracing the inheritance of specific traits or diseases. In human genetics, a pedigree can help illustrate the pattern of genetic inheritance in families over multiple generations. However, it is not a medical term with a specific clinical definition.

Reverse Transcriptase Polymerase Chain Reaction (RT-PCR) is a laboratory technique used in molecular biology to amplify and detect specific DNA sequences. This technique is particularly useful for the detection and quantification of RNA viruses, as well as for the analysis of gene expression.

The process involves two main steps: reverse transcription and polymerase chain reaction (PCR). In the first step, reverse transcriptase enzyme is used to convert RNA into complementary DNA (cDNA) by reading the template provided by the RNA molecule. This cDNA then serves as a template for the PCR amplification step.

In the second step, the PCR reaction uses two primers that flank the target DNA sequence and a thermostable polymerase enzyme to repeatedly copy the targeted cDNA sequence. The reaction mixture is heated and cooled in cycles, allowing the primers to anneal to the template, and the polymerase to extend the new strand. This results in exponential amplification of the target DNA sequence, making it possible to detect even small amounts of RNA or cDNA.

RT-PCR is a sensitive and specific technique that has many applications in medical research and diagnostics, including the detection of viruses such as HIV, hepatitis C virus, and SARS-CoV-2 (the virus that causes COVID-19). It can also be used to study gene expression, identify genetic mutations, and diagnose genetic disorders.

Globins are a group of proteins that contain a heme prosthetic group, which binds and transports oxygen in the blood. The most well-known globin is hemoglobin, which is found in red blood cells and is responsible for carrying oxygen from the lungs to the body's tissues. Other members of the globin family include myoglobin, which is found in muscle tissue and stores oxygen, and neuroglobin and cytoglobin, which are found in the brain and other organs and may have roles in protecting against oxidative stress and hypoxia (low oxygen levels). Globins share a similar structure, with a folded protein surrounding a central heme group. Mutations in globin genes can lead to various diseases, such as sickle cell anemia and thalassemia.

Deoxyribonucleic acid (DNA) is the genetic material present in the cells of organisms where it is responsible for the storage and transmission of hereditary information. DNA is a long molecule that consists of two strands coiled together to form a double helix. Each strand is made up of a series of four nucleotide bases - adenine (A), guanine (G), cytosine (C), and thymine (T) - that are linked together by phosphate and sugar groups. The sequence of these bases along the length of the molecule encodes genetic information, with A always pairing with T and C always pairing with G. This base-pairing allows for the replication and transcription of DNA, which are essential processes in the functioning and reproduction of all living organisms.

Untranslated regions (UTRs) are sections of an mRNA molecule that do not contain information for protein synthesis. There are two types of UTRs: 5' UTR, which is located at the 5' end of the mRNA molecule, and 3' UTR, which is located at the 3' end.

The 5' UTR typically contains regulatory elements that control the translation of the mRNA into protein. These elements can affect the efficiency and timing of translation, as well as the stability of the mRNA molecule. The 5' UTR may also contain upstream open reading frames (uORFs), which are short sequences that can be translated into small peptides and potentially regulate the translation of the main coding sequence.

The length and sequence composition of the 5' UTR can have significant impacts on gene expression, and variations in these regions have been associated with various diseases, including cancer and neurological disorders. Therefore, understanding the structure and function of 5' UTRs is an important area of research in molecular biology and genetics.

Untranslated regions (UTRs) of RNA are the non-coding sequences that are present in mRNA (messenger RNA) molecules, which are located at both the 5' end (5' UTR) and the 3' end (3' UTR) of the mRNA, outside of the coding sequence (CDS). These regions do not get translated into proteins. They contain regulatory elements that play a role in the regulation of gene expression by affecting the stability, localization, and translation efficiency of the mRNA molecule. The 5' UTR typically contains the Shine-Dalgarno sequence in prokaryotes or the Kozak consensus sequence in eukaryotes, which are important for the initiation of translation. The 3' UTR often contains regulatory elements such as AU-rich elements (AREs) and microRNA (miRNA) binding sites that can affect mRNA stability and translation.

Transfection is a term used in molecular biology that refers to the process of deliberately introducing foreign genetic material (DNA, RNA or artificial gene constructs) into cells. This is typically done using chemical or physical methods, such as lipofection or electroporation. Transfection is widely used in research and medical settings for various purposes, including studying gene function, producing proteins, developing gene therapies, and creating genetically modified organisms. It's important to note that transfection is different from transduction, which is the process of introducing genetic material into cells using viruses as vectors.

A sequence deletion in a genetic context refers to the removal or absence of one or more nucleotides (the building blocks of DNA or RNA) from a specific region in a DNA or RNA molecule. This type of mutation can lead to the loss of genetic information, potentially resulting in changes in the function or expression of a gene. If the deletion involves a critical portion of the gene, it can cause diseases, depending on the role of that gene in the body. The size of the deleted sequence can vary, ranging from a single nucleotide to a large segment of DNA.

A plasmid is a small, circular, double-stranded DNA molecule that is separate from the chromosomal DNA of a bacterium or other organism. Plasmids are typically not essential for the survival of the organism, but they can confer beneficial traits such as antibiotic resistance or the ability to degrade certain types of pollutants.

Plasmids are capable of replicating independently of the chromosomal DNA and can be transferred between bacteria through a process called conjugation. They often contain genes that provide resistance to antibiotics, heavy metals, and other environmental stressors. Plasmids have also been engineered for use in molecular biology as cloning vectors, allowing scientists to replicate and manipulate specific DNA sequences.

Plasmids are important tools in genetic engineering and biotechnology because they can be easily manipulated and transferred between organisms. They have been used to produce vaccines, diagnostic tests, and genetically modified organisms (GMOs) for various applications, including agriculture, medicine, and industry.

DNA Sequence Analysis is the systematic determination of the order of nucleotides in a DNA molecule. It is a critical component of modern molecular biology, genetics, and genetic engineering. The process involves determining the exact order of the four nucleotide bases - adenine (A), guanine (G), cytosine (C), and thymine (T) - in a DNA molecule or fragment. This information is used in various applications such as identifying gene mutations, studying evolutionary relationships, developing molecular markers for breeding, and diagnosing genetic diseases.

The process of DNA Sequence Analysis typically involves several steps, including DNA extraction, PCR amplification (if necessary), purification, sequencing reaction, and electrophoresis. The resulting data is then analyzed using specialized software to determine the exact sequence of nucleotides.

In recent years, high-throughput DNA sequencing technologies have revolutionized the field of genomics, enabling the rapid and cost-effective sequencing of entire genomes. This has led to an explosion of genomic data and new insights into the genetic basis of many diseases and traits.

The cell nucleus is a membrane-bound organelle found in the eukaryotic cells (cells with a true nucleus). It contains most of the cell's genetic material, organized as DNA molecules in complex with proteins, RNA molecules, and histones to form chromosomes.

The primary function of the cell nucleus is to regulate and control the activities of the cell, including growth, metabolism, protein synthesis, and reproduction. It also plays a crucial role in the process of mitosis (cell division) by separating and protecting the genetic material during this process. The nuclear membrane, or nuclear envelope, surrounding the nucleus is composed of two lipid bilayers with numerous pores that allow for the selective transport of molecules between the nucleoplasm (nucleus interior) and the cytoplasm (cell exterior).

The cell nucleus is a vital structure in eukaryotic cells, and its dysfunction can lead to various diseases, including cancer and genetic disorders.

A conserved sequence in the context of molecular biology refers to a pattern of nucleotides (in DNA or RNA) or amino acids (in proteins) that has remained relatively unchanged over evolutionary time. These sequences are often functionally important and are highly conserved across different species, indicating strong selection pressure against changes in these regions.

In the case of protein-coding genes, the corresponding amino acid sequence is deduced from the DNA sequence through the genetic code. Conserved sequences in proteins may indicate structurally or functionally important regions, such as active sites or binding sites, that are critical for the protein's activity. Similarly, conserved non-coding sequences in DNA may represent regulatory elements that control gene expression.

Identifying conserved sequences can be useful for inferring evolutionary relationships between species and for predicting the function of unknown genes or proteins.

Trans-splicing is a process in which two different RNA molecules are spliced together to form a single, chimeric RNA molecule. This process involves the removal of introns (non-coding sequences) from both RNA molecules and the ligation of the remaining exons (coding sequences) to create a new RNA molecule that contains genetic information from both original RNAs.

In cis-splicing, which is the more common form of splicing, introns are removed and exons are ligated within the same RNA molecule. However, in trans-splicing, the exons to be ligated come from two separate RNA molecules that have been transcribed from different genes or different regions of the same gene.

Trans-splicing is found in a variety of organisms, including some higher eukaryotes such as humans, where it plays a role in generating genetic diversity and regulating gene expression. It can also occur in certain viruses, where it is used to generate new mRNA molecules that encode for essential viral proteins.

A frameshift mutation is a type of genetic mutation that occurs when the addition or deletion of nucleotides in a DNA sequence is not divisible by three. Since DNA is read in groups of three nucleotides (codons), which each specify an amino acid, this can shift the "reading frame," leading to the insertion or deletion of one or more amino acids in the resulting protein. This can cause a protein to be significantly different from the normal protein, often resulting in a nonfunctional protein and potentially causing disease. Frameshift mutations are typically caused by insertions or deletions of nucleotides, but they can also result from more complex genetic rearrangements.

Molecular cloning is a laboratory technique used to create multiple copies of a specific DNA sequence. This process involves several steps:

1. Isolation: The first step in molecular cloning is to isolate the DNA sequence of interest from the rest of the genomic DNA. This can be done using various methods such as PCR (polymerase chain reaction), restriction enzymes, or hybridization.
2. Vector construction: Once the DNA sequence of interest has been isolated, it must be inserted into a vector, which is a small circular DNA molecule that can replicate independently in a host cell. Common vectors used in molecular cloning include plasmids and phages.
3. Transformation: The constructed vector is then introduced into a host cell, usually a bacterial or yeast cell, through a process called transformation. This can be done using various methods such as electroporation or chemical transformation.
4. Selection: After transformation, the host cells are grown in selective media that allow only those cells containing the vector to grow. This ensures that the DNA sequence of interest has been successfully cloned into the vector.
5. Amplification: Once the host cells have been selected, they can be grown in large quantities to amplify the number of copies of the cloned DNA sequence.

Molecular cloning is a powerful tool in molecular biology and has numerous applications, including the production of recombinant proteins, gene therapy, functional analysis of genes, and genetic engineering.

RNA (Ribonucleic acid) is a single-stranded molecule similar in structure to DNA, involved in the process of protein synthesis in the cell. It acts as a messenger carrying genetic information from DNA to the ribosomes, where proteins are produced.

A neoplasm, on the other hand, is an abnormal growth of cells, which can be benign or malignant. Benign neoplasms are not cancerous and do not invade nearby tissues or spread to other parts of the body. Malignant neoplasms, however, are cancerous and have the potential to invade surrounding tissues and spread to distant sites in the body through a process called metastasis.

Therefore, an 'RNA neoplasm' is not a recognized medical term as RNA is not a type of growth or tumor. However, there are certain types of cancer-causing viruses known as oncoviruses that contain RNA as their genetic material and can cause neoplasms. For example, human T-cell leukemia virus (HTLV-1) and hepatitis C virus (HCV) are RNA viruses that can cause certain types of cancer in humans.

A gene is a specific sequence of nucleotides in DNA that carries genetic information. Genes are the fundamental units of heredity and are responsible for the development and function of all living organisms. They code for proteins or RNA molecules, which carry out various functions within cells and are essential for the structure, function, and regulation of the body's tissues and organs.

Each gene has a specific location on a chromosome, and each person inherits two copies of every gene, one from each parent. Variations in the sequence of nucleotides in a gene can lead to differences in traits between individuals, including physical characteristics, susceptibility to disease, and responses to environmental factors.

Medical genetics is the study of genes and their role in health and disease. It involves understanding how genes contribute to the development and progression of various medical conditions, as well as identifying genetic risk factors and developing strategies for prevention, diagnosis, and treatment.

Protein binding, in the context of medical and biological sciences, refers to the interaction between a protein and another molecule (known as the ligand) that results in a stable complex. This process is often reversible and can be influenced by various factors such as pH, temperature, and concentration of the involved molecules.

In clinical chemistry, protein binding is particularly important when it comes to drugs, as many of them bind to proteins (especially albumin) in the bloodstream. The degree of protein binding can affect a drug's distribution, metabolism, and excretion, which in turn influence its therapeutic effectiveness and potential side effects.

Protein-bound drugs may be less available for interaction with their target tissues, as only the unbound or "free" fraction of the drug is active. Therefore, understanding protein binding can help optimize dosing regimens and minimize adverse reactions.

Regulatory sequences in ribonucleic acid (RNA) refer to specific nucleotide sequences within an RNA molecule that regulate various aspects of gene expression. These sequences do not code for proteins but instead play a crucial role in controlling the transcription, processing, localization, stability, and translation of messenger RNAs (mRNAs) or other non-coding RNAs.

Some common types of regulatory sequences in RNA include:

1. Promoter regions: Although primarily associated with DNA, some RNA polymerase III (Pol III)-transcribed small RNAs have promoter regions within their genes that bind RNA Pol III and transcription factors to initiate transcription.
2. Intron splice sites: These are sequences at the boundaries between exons and introns in a pre-mRNA molecule, guiding the splicing machinery to remove introns and join exons together during mRNA processing.
3. 5' untranslated regions (UTRs): These regions contain various cis-acting elements that can affect translation efficiency, stability, or localization of the mRNA. Examples include upstream AUG regions (uAUGs), internal ribosome entry sites (IRES), and upstream open reading frames (uORFs).
4. 3' untranslated regions (UTRs): These regions also contain cis-acting elements that can influence mRNA stability, translation, or localization. Examples include microRNA (miRNA) binding sites, AU-rich elements (AREs), and G-quadruplex structures.
5. Riboswitches: These are structured RNA elements found in the 5' UTR of certain bacterial mRNAs that can bind small molecules directly, leading to conformational changes that regulate gene expression through transcription termination, translation initiation, or mRNA stability.
6. Cis-regulatory elements (CREs): These are short, conserved sequences within non-coding RNAs that serve as binding sites for trans-acting factors such as RNA-binding proteins (RBPs) and regulatory small RNAs. They can modulate various aspects of RNA metabolism, including processing, transport, stability, and translation.
7. Small nuclear RNAs (snRNAs): These are non-coding RNAs that play crucial roles in pre-mRNA splicing as components of the spliceosome. They recognize specific sequences within introns and facilitate the assembly of the spliceosome complex for accurate splicing.
8. Small nucleolar RNAs (snoRNAs): These are non-coding RNAs that guide chemical modifications, such as methylation or pseudouridination, on other RNA molecules, primarily ribosomal RNAs (rRNAs) and small nuclear RNAs (snRNAs).
9. Piwi-interacting RNAs (piRNAs): These are small non-coding RNAs that associate with PIWI proteins to form the piRNA-induced silencing complex (piRISC) and play essential roles in transposon silencing and epigenetic regulation in germline cells.
10. Long non-coding RNAs (lncRNAs): These are non-coding RNAs longer than 200 nucleotides that can regulate gene expression through various mechanisms, including chromatin remodeling, transcriptional activation or repression, and post-transcriptional regulation. They can act as scaffolds, decoys, guides, or enhancers to modulate the function of proteins, DNA, or other RNA molecules.

These functional RNAs play crucial roles in various aspects of cellular processes, including transcription, splicing, translation, modification, and regulation of gene expression. Dysregulation of these RNAs can lead to diseases, such as cancer, neurodegenerative disorders, and developmental abnormalities. Understanding the biology and functions of these functional RNAs is essential for developing novel therapeutic strategies and diagnostic tools for various diseases.

Transcriptional silencer elements are DNA sequences that bind to specific proteins, known as transcriptional repressors or silencers, to inhibit the transcription of nearby genes. These elements typically recruit chromatin-modifying complexes that alter the structure of the chromatin, making it inaccessible to the transcription machinery. This results in the downregulation or silencing of gene expression. Transcriptional silencer elements can be found in both the promoter and enhancer regions of genes and play crucial roles in regulating various cellular processes, including development, differentiation, and disease pathogenesis.

Base pairing is a specific type of chemical bonding that occurs between complementary base pairs in the nucleic acid molecules DNA and RNA. In DNA, these bases are adenine (A), thymine (T), guanine (G), and cytosine (C). Adenine always pairs with thymine via two hydrogen bonds, while guanine always pairs with cytosine via three hydrogen bonds. This precise base pairing is crucial for the stability of the double helix structure of DNA and for the accurate replication and transcription of genetic information. In RNA, uracil (U) takes the place of thymine and pairs with adenine.

"Spliced leader RNA (SL-RNA)" is a type of RNA molecule that is present in some single-celled eukaryotic organisms, such as trypanosomes and nematodes. In these organisms, spliced leader RNAs play a critical role in the process of gene expression by providing a "leader" sequence that is added to the beginning of messenger RNA (mRNA) molecules during the process of RNA splicing.

SL-RNAs are typically composed of two regions: a conserved 5' " leader" sequence, which is added to the beginning of mRNAs, and a variable 3' " trailer" sequence, which contains the sequences required for recognition and cleavage by the splicing machinery. During RNA splicing, the spliced leader RNA is joined to the target mRNA through a process called trans-splicing, in which the leader sequence of the SL-RNA is ligated to the 5' end of the target mRNA, replacing the original 5' exon.

The addition of the spliced leader sequence to mRNAs can have several important consequences for gene expression. For example, it can help ensure that all mRNAs produced from a given gene contain the same 5' end, even if the gene is transcribed from multiple promoters or undergoes alternative splicing. Additionally, the presence of the conserved leader sequence can serve as a recognition site for RNA-binding proteins, which can regulate mRNA stability, localization, and translation.

Overall, spliced leader RNAs are an important component of the gene expression machinery in many eukaryotic organisms, and their study has provided valuable insights into the mechanisms of RNA processing and regulation.

Heterogeneous Nuclear RNA (hnRNA) is a type of RNA molecule found in the nucleus of eukaryotic cells during the early stages of gene expression. The term "heterogeneous" refers to the diverse range of sizes and structures that these RNAs exhibit, which can vary from several hundred to tens of thousands of nucleotides in length.

HnRNA is transcribed from DNA templates by the enzyme RNA polymerase II and includes both introns (non-coding sequences) and exons (coding sequences) that will eventually be spliced together to form mature mRNA molecules. HnRNA also contains additional sequences, such as 5' cap structures and 3' poly(A) tails, which are added during post-transcriptional processing.

Because hnRNA is a precursor to mature mRNA, it is often used as a marker for transcriptionally active genes. However, not all hnRNA molecules are ultimately processed into mRNA; some may be degraded or converted into other types of RNA, such as microRNAs or long non-coding RNAs.

Overall, hnRNA plays a critical role in the regulation and expression of genes in eukaryotic cells.

Regulatory sequences in nucleic acid refer to specific DNA or RNA segments that control the spatial and temporal expression of genes without encoding proteins. They are crucial for the proper functioning of cells as they regulate various cellular processes such as transcription, translation, mRNA stability, and localization. Regulatory sequences can be found in both coding and non-coding regions of DNA or RNA.

Some common types of regulatory sequences in nucleic acid include:

1. Promoters: DNA sequences typically located upstream of the gene that provide a binding site for RNA polymerase and transcription factors to initiate transcription.
2. Enhancers: DNA sequences, often located at a distance from the gene, that enhance transcription by binding to specific transcription factors and increasing the recruitment of RNA polymerase.
3. Silencers: DNA sequences that repress transcription by binding to specific proteins that inhibit the recruitment of RNA polymerase or promote chromatin compaction.
4. Intron splice sites: Specific nucleotide sequences within introns (non-coding regions) that mark the boundaries between exons (coding regions) and are essential for correct splicing of pre-mRNA.
5. 5' untranslated regions (UTRs): Regions located at the 5' end of an mRNA molecule that contain regulatory elements affecting translation efficiency, stability, and localization.
6. 3' untranslated regions (UTRs): Regions located at the 3' end of an mRNA molecule that contain regulatory elements influencing translation termination, stability, and localization.
7. miRNA target sites: Specific sequences in mRNAs that bind to microRNAs (miRNAs) leading to translational repression or degradation of the target mRNA.

"Poly A" is an abbreviation for "poly(A) tail" or "polyadenylation." It refers to the addition of multiple adenine (A) nucleotides to the 3' end of eukaryotic mRNA molecules during the process of transcription. This poly(A) tail plays a crucial role in various aspects of mRNA metabolism, including stability, transport, and translation. The length of the poly(A) tail can vary from around 50 to 250 nucleotides depending on the cell type and developmental stage.

A nonsense codon is a sequence of three nucleotides in DNA or RNA that does not code for an amino acid. Instead, it signals the end of the protein-coding region of a gene and triggers the termination of translation, the process by which the genetic code is translated into a protein.

In DNA, the nonsense codons are UAA, UAG, and UGA, which are also known as "stop codons." When these codons are encountered during translation, they cause the release of the newly synthesized polypeptide chain from the ribosome, bringing the process of protein synthesis to a halt.

Nonsense mutations are changes in the DNA sequence that result in the appearance of a nonsense codon where an amino acid-coding codon used to be. These types of mutations can lead to premature termination of translation and the production of truncated, nonfunctional proteins, which can cause genetic diseases or contribute to cancer development.

Ribonuclease H (RNase H) is an enzyme that specifically degrades the RNA portion of an RNA-DNA hybrid. It cleaves the phosphodiester bond between the ribose sugar and the phosphate group in the RNA strand, leaving the DNA strand intact. This enzyme plays a crucial role in several cellular processes, including DNA replication, repair, and transcription.

There are two main types of RNase H: type 1 and type 2. Type 1 RNase H is found in both prokaryotic and eukaryotic cells, while type 2 RNase H is primarily found in eukaryotes. The primary function of RNase H is to remove RNA primers that are synthesized during DNA replication. These RNA primers are replaced with DNA nucleotides by another enzyme called polymerase δ, leaving behind a gap in the DNA strand. RNase H then cleaves the RNA-DNA hybrid, allowing for the repair of the gap and the completion of DNA replication.

RNase H has also been implicated in the regulation of gene expression, as it can degrade RNA-DNA hybrids formed during transcription. This process, known as transcription-coupled RNA decay, helps to prevent the accumulation of aberrant RNA molecules and ensures proper gene expression.

In addition to its cellular functions, RNase H has been studied for its potential therapeutic applications. For example, inhibitors of RNase H have been shown to have antiviral activity against HIV-1, as they prevent the degradation of viral RNA during reverse transcription. On the other hand, activators of RNase H have been explored as a means to enhance the efficiency of RNA interference (RNAi) therapies by promoting the degradation of target RNA molecules.

Single-strand specific DNA and RNA endonucleases are enzymes that cleave or cut single-stranded DNA or RNA molecules at specific sites, leaving a free 3'-hydroxyl group and a 5'-phosphate group on the resulting fragments. These enzymes recognize and bind to particular nucleotide sequences or structural motifs in single-stranded nucleic acids, making them useful tools for various molecular biology techniques such as DNA and RNA mapping, sequencing, and manipulation.

Examples of single-strand specific endonucleases include S1 nuclease (specific to single-stranded DNA), mung bean nuclease (specific to single-stranded DNA with a preference for 3'-overhangs), and RNase A (specific to single-stranded RNA). These enzymes have distinct substrate specificities, cleavage patterns, and optimal reaction conditions, which should be carefully considered when selecting them for specific applications.

"Saccharomyces cerevisiae" is not typically considered a medical term, but it is a scientific name used in the field of microbiology. It refers to a species of yeast that is commonly used in various industrial processes, such as baking and brewing. It's also widely used in scientific research due to its genetic tractability and eukaryotic cellular organization.

However, it does have some relevance to medical fields like medicine and nutrition. For example, certain strains of S. cerevisiae are used as probiotics, which can provide health benefits when consumed. They may help support gut health, enhance the immune system, and even assist in the digestion of certain nutrients.

In summary, "Saccharomyces cerevisiae" is a species of yeast with various industrial and potential medical applications.

I'm sorry for any confusion, but "Ficusin" is not a recognized term in medical or scientific literature. It appears to be a made-up name. Ficus is a genus of plants that includes many species commonly known as fig trees, but there is no specific "Ficusin" compound derived from this plant or used in medical contexts. If you have more information about where you encountered this term or if it's related to a specific context, I would be happy to help further!

Base composition in genetics refers to the relative proportion of the four nucleotide bases (adenine, thymine, guanine, and cytosine) in a DNA or RNA molecule. In DNA, adenine pairs with thymine, and guanine pairs with cytosine, so the base composition is often expressed in terms of the ratio of adenine + thymine (A-T) to guanine + cytosine (G-C). This ratio can vary between species and even between different regions of the same genome. The base composition can provide important clues about the function, evolution, and structure of genetic material.

Sequence homology, amino acid, refers to the similarity in the order of amino acids in a protein or a portion of a protein between two or more species. This similarity can be used to infer evolutionary relationships and functional similarities between proteins. The higher the degree of sequence homology, the more likely it is that the proteins are related and have similar functions. Sequence homology can be determined through various methods such as pairwise alignment or multiple sequence alignment, which compare the sequences and calculate a score based on the number and type of matching amino acids.

Genetic enhancer elements are DNA sequences that increase the transcription of specific genes. They work by binding to regulatory proteins called transcription factors, which in turn recruit RNA polymerase II, the enzyme responsible for transcribing DNA into messenger RNA (mRNA). This results in the activation of gene transcription and increased production of the protein encoded by that gene.

Enhancer elements can be located upstream, downstream, or even within introns of the genes they regulate, and they can act over long distances along the DNA molecule. They are an important mechanism for controlling gene expression in a tissue-specific and developmental stage-specific manner, allowing for the precise regulation of gene activity during embryonic development and throughout adult life.

It's worth noting that genetic enhancer elements are often referred to simply as "enhancers," and they are distinct from other types of regulatory DNA sequences such as promoters, silencers, and insulators.

'Gene expression regulation' refers to the processes that control whether, when, and where a particular gene is expressed, meaning the production of a specific protein or functional RNA encoded by that gene. This complex mechanism can be influenced by various factors such as transcription factors, chromatin remodeling, DNA methylation, non-coding RNAs, and post-transcriptional modifications, among others. Proper regulation of gene expression is crucial for normal cellular function, development, and maintaining homeostasis in living organisms. Dysregulation of gene expression can lead to various diseases, including cancer and genetic disorders.

A phenotype is the physical or biochemical expression of an organism's genes, or the observable traits and characteristics resulting from the interaction of its genetic constitution (genotype) with environmental factors. These characteristics can include appearance, development, behavior, and resistance to disease, among others. Phenotypes can vary widely, even among individuals with identical genotypes, due to differences in environmental influences, gene expression, and genetic interactions.

Tertiary protein structure refers to the three-dimensional arrangement of all the elements (polypeptide chains) of a single protein molecule. It is the highest level of structural organization and results from interactions between various side chains (R groups) of the amino acids that make up the protein. These interactions, which include hydrogen bonds, ionic bonds, van der Waals forces, and disulfide bridges, give the protein its unique shape and stability, which in turn determines its function. The tertiary structure of a protein can be stabilized by various factors such as temperature, pH, and the presence of certain ions. Any changes in these factors can lead to denaturation, where the protein loses its tertiary structure and thus its function.

An allele is a variant form of a gene that is located at a specific position on a specific chromosome. Alleles are alternative forms of the same gene that arise by mutation and are found at the same locus or position on homologous chromosomes.

Each person typically inherits two copies of each gene, one from each parent. If the two alleles are identical, a person is said to be homozygous for that trait. If the alleles are different, the person is heterozygous.

For example, the ABO blood group system has three alleles, A, B, and O, which determine a person's blood type. If a person inherits two A alleles, they will have type A blood; if they inherit one A and one B allele, they will have type AB blood; if they inherit two B alleles, they will have type B blood; and if they inherit two O alleles, they will have type O blood.

Alleles can also influence traits such as eye color, hair color, height, and other physical characteristics. Some alleles are dominant, meaning that only one copy of the allele is needed to express the trait, while others are recessive, meaning that two copies of the allele are needed to express the trait.

In genetics, sequence alignment is the process of arranging two or more DNA, RNA, or protein sequences to identify regions of similarity or homology between them. This is often done using computational methods to compare the nucleotide or amino acid sequences and identify matching patterns, which can provide insight into evolutionary relationships, functional domains, or potential genetic disorders. The alignment process typically involves adjusting gaps and mismatches in the sequences to maximize the similarity between them, resulting in an aligned sequence that can be visually represented and analyzed.

Oligoribonucleotides are short, synthetic chains of ribonucleotides, which are the building blocks of RNA (ribonucleic acid). These chains typically contain fewer than 20 ribonucleotide units, and can be composed of all four types of nucleotides found in RNA: adenine (A), uracil (U), guanine (G), and cytosine (C). They are often used in research for various purposes, such as studying RNA function, regulating gene expression, or serving as potential therapeutic agents.

Cross-linking reagents are chemical agents that are used to create covalent bonds between two or more molecules, creating a network of interconnected molecules known as a cross-linked structure. In the context of medical and biological research, cross-linking reagents are often used to stabilize protein structures, study protein-protein interactions, and develop therapeutic agents.

Cross-linking reagents work by reacting with functional groups on adjacent molecules, such as amino groups (-NH2) or sulfhydryl groups (-SH), to form a covalent bond between them. This can help to stabilize protein structures and prevent them from unfolding or aggregating.

There are many different types of cross-linking reagents, each with its own specificity and reactivity. Some common examples include glutaraldehyde, formaldehyde, disuccinimidyl suberate (DSS), and bis(sulfosuccinimidyl) suberate (BS3). The choice of cross-linking reagent depends on the specific application and the properties of the molecules being cross-linked.

It is important to note that cross-linking reagents can also have unintended effects, such as modifying or disrupting the function of the proteins they are intended to stabilize. Therefore, it is essential to use them carefully and with appropriate controls to ensure accurate and reliable results.

Northern blotting is a laboratory technique used in molecular biology to detect and analyze specific RNA molecules (such as mRNA) in a mixture of total RNA extracted from cells or tissues. This technique is called "Northern" blotting because it is analogous to the Southern blotting method, which is used for DNA detection.

The Northern blotting procedure involves several steps:

1. Electrophoresis: The total RNA mixture is first separated based on size by running it through an agarose gel using electrical current. This separates the RNA molecules according to their length, with smaller RNA fragments migrating faster than larger ones.

2. Transfer: After electrophoresis, the RNA bands are denatured (made single-stranded) and transferred from the gel onto a nitrocellulose or nylon membrane using a technique called capillary transfer or vacuum blotting. This step ensures that the order and relative positions of the RNA fragments are preserved on the membrane, similar to how they appear in the gel.

3. Cross-linking: The RNA is then chemically cross-linked to the membrane using UV light or heat treatment, which helps to immobilize the RNA onto the membrane and prevent it from washing off during subsequent steps.

4. Prehybridization: Before adding the labeled probe, the membrane is prehybridized in a solution containing blocking agents (such as salmon sperm DNA or yeast tRNA) to minimize non-specific binding of the probe to the membrane.

5. Hybridization: A labeled nucleic acid probe, specific to the RNA of interest, is added to the prehybridization solution and allowed to hybridize (form base pairs) with its complementary RNA sequence on the membrane. The probe can be either a DNA or an RNA molecule, and it is typically labeled with a radioactive isotope (such as ³²P) or a non-radioactive label (such as digoxigenin).

6. Washing: After hybridization, the membrane is washed to remove unbound probe and reduce background noise. The washing conditions (temperature, salt concentration, and detergent concentration) are optimized based on the stringency required for specific hybridization.

7. Detection: The presence of the labeled probe is then detected using an appropriate method, depending on the type of label used. For radioactive probes, this typically involves exposing the membrane to X-ray film or a phosphorimager screen and analyzing the resulting image. For non-radioactive probes, detection can be performed using colorimetric, chemiluminescent, or fluorescent methods.

8. Data analysis: The intensity of the signal is quantified and compared to controls (such as housekeeping genes) to determine the relative expression level of the RNA of interest. This information can be used for various purposes, such as identifying differentially expressed genes in response to a specific treatment or comparing gene expression levels across different samples or conditions.

Protein biosynthesis is the process by which cells generate new proteins. It involves two major steps: transcription and translation. Transcription is the process of creating a complementary RNA copy of a sequence of DNA. This RNA copy, or messenger RNA (mRNA), carries the genetic information to the site of protein synthesis, the ribosome. During translation, the mRNA is read by transfer RNA (tRNA) molecules, which bring specific amino acids to the ribosome based on the sequence of nucleotides in the mRNA. The ribosome then links these amino acids together in the correct order to form a polypeptide chain, which may then fold into a functional protein. Protein biosynthesis is essential for the growth and maintenance of all living organisms.

A nucleic acid database is a type of biological database that contains sequence, structure, and functional information about nucleic acids, such as DNA and RNA. These databases are used in various fields of biology, including genomics, molecular biology, and bioinformatics, to store, search, and analyze nucleic acid data.

Some common types of nucleic acid databases include:

1. Nucleotide sequence databases: These databases contain the primary nucleotide sequences of DNA and RNA molecules from various organisms. Examples include GenBank, EMBL-Bank, and DDBJ.
2. Structure databases: These databases contain three-dimensional structures of nucleic acids determined by experimental methods such as X-ray crystallography or nuclear magnetic resonance (NMR) spectroscopy. Examples include the Protein Data Bank (PDB) and the Nucleic Acid Database (NDB).
3. Functional databases: These databases contain information about the functions of nucleic acids, such as their roles in gene regulation, transcription, and translation. Examples include the Gene Ontology (GO) database and the RegulonDB.
4. Genome databases: These databases contain genomic data for various organisms, including whole-genome sequences, gene annotations, and genetic variations. Examples include the Human Genome Database (HGD) and the Ensembl Genome Browser.
5. Comparative databases: These databases allow for the comparison of nucleic acid sequences or structures across different species or conditions. Examples include the Comparative RNA Web (CRW) Site and the Sequence Alignment and Modeling (SAM) system.

Nucleic acid databases are essential resources for researchers to study the structure, function, and evolution of nucleic acids, as well as to develop new tools and methods for analyzing and interpreting nucleic acid data.

3' Untranslated Regions (3' UTRs) are segments of messenger RNA (mRNA) that do not code for proteins. They are located after the last exon, which contains the coding sequence for a protein, and before the poly-A tail in eukaryotic mRNAs.

The 3' UTR plays several important roles in regulating gene expression, including:

1. Stability of mRNA: The 3' UTR contains sequences that can bind to proteins that either stabilize or destabilize the mRNA, thereby controlling its half-life and abundance.
2. Localization of mRNA: Some 3' UTRs contain sequences that direct the localization of the mRNA to specific cellular compartments, such as the synapse in neurons.
3. Translation efficiency: The 3' UTR can also contain regulatory elements that affect the translation efficiency of the mRNA into protein. For example, microRNAs (miRNAs) can bind to complementary sequences in the 3' UTR and inhibit translation or promote degradation of the mRNA.
4. Alternative polyadenylation: The 3' UTR can also contain multiple alternative polyadenylation sites, which can lead to different lengths of the 3' UTR and affect gene expression.

Overall, the 3' UTR plays a critical role in post-transcriptional regulation of gene expression, and mutations or variations in the 3' UTR can contribute to human diseases.

Nucleic acid hybridization is a process in molecular biology where two single-stranded nucleic acids (DNA, RNA) with complementary sequences pair together to form a double-stranded molecule through hydrogen bonding. The strands can be from the same type of nucleic acid or different types (i.e., DNA-RNA or DNA-cDNA). This process is commonly used in various laboratory techniques, such as Southern blotting, Northern blotting, polymerase chain reaction (PCR), and microarray analysis, to detect, isolate, and analyze specific nucleic acid sequences. The hybridization temperature and conditions are critical to ensure the specificity of the interaction between the two strands.

RNA Polymerase III is a type of enzyme that carries out the transcription of DNA into RNA, specifically functioning in the synthesis of small, stable RNAs. These RNAs include 5S rRNA, transfer RNAs (tRNAs), and other small nuclear RNAs (snRNAs). The enzyme recognizes specific promoter sequences in DNA and catalyzes the formation of phosphodiester bonds between ribonucleotides to create a complementary RNA strand. RNA Polymerase III is essential for protein synthesis and cell survival, and its activity is tightly regulated within the cell.

Restriction mapping is a technique used in molecular biology to identify the location and arrangement of specific restriction endonuclease recognition sites within a DNA molecule. Restriction endonucleases are enzymes that cut double-stranded DNA at specific sequences, producing fragments of various lengths. By digesting the DNA with different combinations of these enzymes and analyzing the resulting fragment sizes through techniques such as agarose gel electrophoresis, researchers can generate a restriction map - a visual representation of the locations and distances between recognition sites on the DNA molecule. This information is crucial for various applications, including cloning, genome analysis, and genetic engineering.

Computational biology is a branch of biology that uses mathematical and computational methods to study biological data, models, and processes. It involves the development and application of algorithms, statistical models, and computational approaches to analyze and interpret large-scale molecular and phenotypic data from genomics, transcriptomics, proteomics, metabolomics, and other high-throughput technologies. The goal is to gain insights into biological systems and processes, develop predictive models, and inform experimental design and hypothesis testing in the life sciences. Computational biology encompasses a wide range of disciplines, including bioinformatics, systems biology, computational genomics, network biology, and mathematical modeling of biological systems.

Promoter regions in genetics refer to specific DNA sequences located near the transcription start site of a gene. They serve as binding sites for RNA polymerase and various transcription factors that regulate the initiation of gene transcription. These regulatory elements help control the rate of transcription and, therefore, the level of gene expression. Promoter regions can be composed of different types of sequences, such as the TATA box and CAAT box, and their organization and composition can vary between different genes and species.

Gene expression regulation, viral, refers to the processes that control the production of viral gene products, such as proteins and nucleic acids, during the viral life cycle. This can involve both viral and host cell factors that regulate transcription, RNA processing, translation, and post-translational modifications of viral genes.

Viral gene expression regulation is critical for the virus to replicate and produce progeny virions. Different types of viruses have evolved diverse mechanisms to regulate their gene expression, including the use of promoters, enhancers, transcription factors, RNA silencing, and epigenetic modifications. Understanding these regulatory processes can provide insights into viral pathogenesis and help in the development of antiviral therapies.

A missense mutation is a type of point mutation in which a single nucleotide change results in the substitution of a different amino acid in the protein that is encoded by the affected gene. This occurs when the altered codon (a sequence of three nucleotides that corresponds to a specific amino acid) specifies a different amino acid than the original one. The function and/or stability of the resulting protein may be affected, depending on the type and location of the missense mutation. Missense mutations can have various effects, ranging from benign to severe, depending on the importance of the changed amino acid for the protein's structure or function.

An open reading frame (ORF) is a continuous stretch of DNA or RNA sequence that has the potential to be translated into a protein. It begins with a start codon (usually "ATG" in DNA, which corresponds to "AUG" in RNA) and ends with a stop codon ("TAA", "TAG", or "TGA" in DNA; "UAA", "UAG", or "UGA" in RNA). The sequence between these two points is called a coding sequence (CDS), which, when transcribed into mRNA and translated into amino acids, forms a polypeptide chain.

In eukaryotic cells, ORFs can be located in either protein-coding genes or non-coding regions of the genome. In prokaryotic cells, multiple ORFs may be present on a single strand of DNA, often organized into operons that are transcribed together as a single mRNA molecule.

It's important to note that not all ORFs necessarily represent functional proteins; some may be pseudogenes or result from errors in genome annotation. Therefore, additional experimental evidence is typically required to confirm the expression and functionality of a given ORF.

Polypyrimidine Tract-Binding Protein (PTB) is a protein that binds to specific sequences of RNA molecules, including polypyrimidine tracts, which are stretches of uracil and cytosine nucleotides. PTB plays a crucial role in post-transcriptional regulation of gene expression by affecting alternative splicing, polyadenylation, stability, and translation of target RNAs. It has been implicated in various cellular processes, such as neuronal development, differentiation, and oncogenesis. Mutations in the PTB gene have been associated with several human diseases, including neurological disorders and cancer.

Site-directed mutagenesis is a molecular biology technique used to introduce specific and targeted changes to a specific DNA sequence. This process involves creating a new variant of a gene or a specific region of interest within a DNA molecule by introducing a planned, deliberate change, or mutation, at a predetermined site within the DNA sequence.

The methodology typically involves the use of molecular tools such as PCR (polymerase chain reaction), restriction enzymes, and/or ligases to introduce the desired mutation(s) into a plasmid or other vector containing the target DNA sequence. The resulting modified DNA molecule can then be used to transform host cells, allowing for the production of large quantities of the mutated gene or protein for further study.

Site-directed mutagenesis is a valuable tool in basic research, drug discovery, and biotechnology applications where specific changes to a DNA sequence are required to understand gene function, investigate protein structure/function relationships, or engineer novel biological properties into existing genes or proteins.

RNA Polymerase I is a type of enzyme that carries out the transcription of ribosomal RNA (rRNA) genes in eukaryotic cells. These enzymes are responsible for synthesizing the rRNA molecules, which are crucial components of ribosomes, the cellular structures where protein synthesis occurs. RNA Polymerase I is found in the nucleolus, a specialized region within the nucleus of eukaryotic cells, and it primarily transcribes the 5S, 18S, and 28S rRNA genes. The enzyme binds to the promoter regions of these genes and synthesizes the rRNA molecules by adding ribonucleotides in a template-directed manner, using DNA as a template. This process is essential for maintaining normal cellular function and for the production of proteins required for growth, development, and homeostasis.

A genetic template refers to the sequence of DNA or RNA that contains the instructions for the development and function of an organism or any of its components. These templates provide the code for the synthesis of proteins and other functional molecules, and determine many of the inherited traits and characteristics of an individual. In this sense, genetic templates serve as the blueprint for life and are passed down from one generation to the next through the process of reproduction.

In molecular biology, the term "template" is used to describe the strand of DNA or RNA that serves as a guide or pattern for the synthesis of a complementary strand during processes such as transcription and replication. During transcription, the template strand of DNA is transcribed into a complementary RNA molecule, while during replication, each parental DNA strand serves as a template for the synthesis of a new complementary strand.

In genetic engineering and synthetic biology, genetic templates can be manipulated and modified to introduce new functions or alter existing ones in organisms. This is achieved through techniques such as gene editing, where specific sequences in the genetic template are targeted and altered using tools like CRISPR-Cas9. Overall, genetic templates play a crucial role in shaping the structure, function, and evolution of all living organisms.

'RNA, Nuclear' refers to Ribonucleic Acid that is located within the nucleus of a eukaryotic cell. It plays a crucial role in the process of gene expression, specifically in the transcription of DNA into messenger RNA (mRNA). During this process, a segment of DNA is copied into a complementary RNA strand, known as a primary transcript. This primary transcript then undergoes various processing steps within the nucleus, such as splicing and capping, to produce mature, functional mRNA. Nuclear RNA also includes other non-coding RNAs, such as ribosomal RNA (rRNA), transfer RNA (tRNA), and small nuclear RNA (snRNA), which are involved in various cellular processes including protein synthesis and regulation of gene expression.

A gene product is the biochemical material, such as a protein or RNA, that is produced by the expression of a gene. The term "gene products, rev" is not a standard medical or scientific term, and its meaning is not immediately clear without additional context. However, "rev" is sometimes used in molecular biology to denote reverse orientation or transcription, so "gene products, rev" might refer to RNA molecules that are produced when a gene is transcribed in the opposite direction from what is typically observed.

It's important to note that not all genes produce protein products; some genes code for RNAs that have regulatory or structural functions, while others produce both proteins and RNA molecules. The study of gene products and their functions is an important area of research in molecular biology and genetics, as it can provide insights into the underlying mechanisms of genetic diseases and other biological processes.

Beta-crystallin A chain is a protein that is a component of the beta-crystallin complex, which is a major structural element of the vertebrate eye lens. The beta-crystallins are organized into two subfamilies, called beta-A and beta-B, based on their primary structures.

The beta-crystallin A chain is a polypeptide chain that contains approximately 100 amino acids and has a molecular weight of around 12 kilodaltons. It is encoded by the CRYBA1 gene in humans. The protein is characterized by four conserved domains, called Greek key motifs, which are involved in the formation of the quaternary structure of the beta-crystallin complex.

Mutations in the CRYBA1 gene have been associated with various forms of congenital cataracts, which are clouding of the eye lens that can lead to visual impairment or blindness. The precise function of beta-crystallins is not fully understood, but they are thought to play a role in maintaining the transparency and refractive properties of the eye lens.

Transcription factors are proteins that play a crucial role in regulating gene expression by controlling the transcription of DNA to messenger RNA (mRNA). They function by binding to specific DNA sequences, known as response elements, located in the promoter region or enhancer regions of target genes. This binding can either activate or repress the initiation of transcription, depending on the properties and interactions of the particular transcription factor. Transcription factors often act as part of a complex network of regulatory proteins that determine the precise spatiotemporal patterns of gene expression during development, differentiation, and homeostasis in an organism.

Oligonucleotides are short sequences of nucleotides, the building blocks of DNA and RNA. They typically contain fewer than 100 nucleotides, and can be synthesized chemically to have specific sequences. Oligonucleotides are used in a variety of applications in molecular biology, including as probes for detecting specific DNA or RNA sequences, as inhibitors of gene expression, and as components of diagnostic tests and therapies. They can also be used in the study of protein-nucleic acid interactions and in the development of new drugs.

A heterozygote is an individual who has inherited two different alleles (versions) of a particular gene, one from each parent. This means that the individual's genotype for that gene contains both a dominant and a recessive allele. The dominant allele will be expressed phenotypically (outwardly visible), while the recessive allele may or may not have any effect on the individual's observable traits, depending on the specific gene and its function. Heterozygotes are often represented as 'Aa', where 'A' is the dominant allele and 'a' is the recessive allele.

Molecular evolution is the process of change in the DNA sequence or protein structure over time, driven by mechanisms such as mutation, genetic drift, gene flow, and natural selection. It refers to the evolutionary study of changes in DNA, RNA, and proteins, and how these changes accumulate and lead to new species and diversity of life. Molecular evolution can be used to understand the history and relationships among different organisms, as well as the functional consequences of genetic changes.

A guide RNA (gRNA) is not a type of RNA itself, but rather a term used to describe various types of RNAs that guide other molecules to specific target sites in the genome or transcriptome. The most well-known example of a guide RNA is the CRISPR RNA (crRNA) used in the CRISPR-Cas system for targeted gene editing.

The crRNA contains a sequence complementary to the target DNA or RNA, and it guides the Cas endonuclease to the correct location in the genome where cleavage and modification can occur. Other types of guide RNAs include small interfering RNAs (siRNAs) and microRNAs (miRNAs), which guide the RNA-induced silencing complex (RISC) to specific mRNA targets for degradation or translational repression.

Overall, guide RNAs play crucial roles in various cellular processes, including gene regulation, genome editing, and defense against foreign genetic elements.

Endoribonucleases are enzymes that cleave RNA molecules internally, meaning they cut the phosphodiester bond between nucleotides within the RNA chain. These enzymes play crucial roles in various cellular processes, such as RNA processing, degradation, and quality control. Different endoribonucleases recognize specific sequences or structural features in RNA substrates, allowing them to target particular regions for cleavage. Some well-known examples of endoribonucleases include RNase III, RNase T1, and RNase A, each with distinct substrate preferences and functions.

Genetic variation refers to the differences in DNA sequences among individuals and populations. These variations can result from mutations, genetic recombination, or gene flow between populations. Genetic variation is essential for evolution by providing the raw material upon which natural selection acts. It can occur within a single gene, between different genes, or at larger scales, such as differences in the number of chromosomes or entire sets of chromosomes. The study of genetic variation is crucial in understanding the genetic basis of diseases and traits, as well as the evolutionary history and relationships among species.

28S ribosomal RNA (rRNA) is a component of the large subunit of the eukaryotic ribosome, which is the site of protein synthesis in the cell. The ribosome is composed of two subunits, one large and one small, that come together around an mRNA molecule to translate it into a protein.

The 28S rRNA is a type of rRNA that is found in the large subunit of the eukaryotic ribosome, along with the 5S and 5.8S rRNAs. Together, these rRNAs make up the structural framework of the ribosome and play a crucial role in the process of translation.

The 28S rRNA is synthesized in the nucleolus as a precursor RNA (pre-rRNA) that undergoes several processing steps, including cleavage and modification, to produce the mature 28S rRNA molecule. The length of the 28S rRNA varies between species, but it is typically around 4700-5000 nucleotides long in humans.

Abnormalities in the structure or function of the 28S rRNA can lead to defects in protein synthesis and have been implicated in various diseases, including cancer and neurological disorders.

Mutagenesis is the process by which the genetic material (DNA or RNA) of an organism is changed in a way that can alter its phenotype, or observable traits. These changes, known as mutations, can be caused by various factors such as chemicals, radiation, or viruses. Some mutations may have no effect on the organism, while others can cause harm, including diseases and cancer. Mutagenesis is a crucial area of study in genetics and molecular biology, with implications for understanding evolution, genetic disorders, and the development of new medical treatments.

Gene expression is the process by which the information encoded in a gene is used to synthesize a functional gene product, such as a protein or RNA molecule. This process involves several steps: transcription, RNA processing, and translation. During transcription, the genetic information in DNA is copied into a complementary RNA molecule, known as messenger RNA (mRNA). The mRNA then undergoes RNA processing, which includes adding a cap and tail to the mRNA and splicing out non-coding regions called introns. The resulting mature mRNA is then translated into a protein on ribosomes in the cytoplasm through the process of translation.

The regulation of gene expression is a complex and highly controlled process that allows cells to respond to changes in their environment, such as growth factors, hormones, and stress signals. This regulation can occur at various stages of gene expression, including transcriptional activation or repression, RNA processing, mRNA stability, and translation. Dysregulation of gene expression has been implicated in many diseases, including cancer, genetic disorders, and neurological conditions.

Rev (Regulator of Expression of Virion) gene products of the Human Immunodeficiency Virus (HIV) refer to the proteins encoded by the rev gene, which is one of the accessory genes of HIV. The rev protein plays a crucial role in the regulation of viral gene expression and replication.

During the early stages of HIV infection, the viral genome is transcribed into full-length RNA transcripts that serve as both messenger RNA (mRNA) for protein synthesis and genomic RNA for packaging into new virus particles. However, these full-length transcripts are unable to exit the nucleus and undergo translation due to their large size and the presence of intronic sequences.

The rev protein functions as a nuclear export factor that binds to specific Rev Response Elements (RRE) present within these full-length transcripts, allowing them to be transported out of the nucleus into the cytoplasm for translation and packaging. By regulating the nuclear export of viral RNA, rev ensures proper expression of viral genes required for virus replication and assembly.

Rev protein also plays a role in downregulating the production of early viral proteins, such as Tat and Nef, while promoting the expression of late viral proteins, like Env and Gag, which are necessary for virion assembly and release. This temporal regulation of gene expression is critical for efficient HIV replication and pathogenesis.

Tetrahymena is not a medical term itself, but it is a genus of unicellular organisms known as ciliates. They are commonly found in freshwater environments and can be studied in the field of biology and microbiology. Some species of Tetrahymena have been used in scientific research, including studies on genetics, cell division, and protein function. It is not a term that would typically be used in a medical context.

Expressed Sequence Tags (ESTs) are short, single-pass DNA sequences that are derived from cDNA libraries. They represent a quick and cost-effective method for large-scale sequencing of gene transcripts and provide an unbiased view of the genes being actively expressed in a particular tissue or developmental stage. ESTs can be used to identify and study new genes, to analyze patterns of gene expression, and to develop molecular markers for genetic mapping and genome analysis.

A gene is a segment of DNA that contains the instructions for the development and function of an organism. Genes are the basic units of inheritance, and they determine many of an individual's characteristics, such as eye color, hair color, and height.

In revised terminology, "genes" can be defined more specifically as a DNA sequence that codes for a functional RNA molecule or a protein. This includes both coding sequences (exons) and non-coding sequences (introns). The revised definition also acknowledges the role of regulatory elements, such as promoters and enhancers, which are DNA sequences that control the expression of genes.

Additionally, it is important to note that genes can exist in different forms, known as alleles, which can result in variations in traits among individuals. Some genes may also have multiple functions or be involved in complex genetic interactions, contributing to the complexity of genetics and inheritance.

Virus replication is the process by which a virus produces copies or reproduces itself inside a host cell. This involves several steps:

1. Attachment: The virus attaches to a specific receptor on the surface of the host cell.
2. Penetration: The viral genetic material enters the host cell, either by invagination of the cell membrane or endocytosis.
3. Uncoating: The viral genetic material is released from its protective coat (capsid) inside the host cell.
4. Replication: The viral genetic material uses the host cell's machinery to produce new viral components, such as proteins and nucleic acids.
5. Assembly: The newly synthesized viral components are assembled into new virus particles.
6. Release: The newly formed viruses are released from the host cell, often through lysis (breaking) of the cell membrane or by budding off the cell membrane.

The specific mechanisms and details of virus replication can vary depending on the type of virus. Some viruses, such as DNA viruses, use the host cell's DNA polymerase to replicate their genetic material, while others, such as RNA viruses, use their own RNA-dependent RNA polymerase or reverse transcriptase enzymes. Understanding the process of virus replication is important for developing antiviral therapies and vaccines.

"Cells, cultured" is a medical term that refers to cells that have been removed from an organism and grown in controlled laboratory conditions outside of the body. This process is called cell culture and it allows scientists to study cells in a more controlled and accessible environment than they would have inside the body. Cultured cells can be derived from a variety of sources, including tissues, organs, or fluids from humans, animals, or cell lines that have been previously established in the laboratory.

Cell culture involves several steps, including isolation of the cells from the tissue, purification and characterization of the cells, and maintenance of the cells in appropriate growth conditions. The cells are typically grown in specialized media that contain nutrients, growth factors, and other components necessary for their survival and proliferation. Cultured cells can be used for a variety of purposes, including basic research, drug development and testing, and production of biological products such as vaccines and gene therapies.

It is important to note that cultured cells may behave differently than they do in the body, and results obtained from cell culture studies may not always translate directly to human physiology or disease. Therefore, it is essential to validate findings from cell culture experiments using additional models and ultimately in clinical trials involving human subjects.

Chromosome mapping, also known as physical mapping, is the process of determining the location and order of specific genes or genetic markers on a chromosome. This is typically done by using various laboratory techniques to identify landmarks along the chromosome, such as restriction enzyme cutting sites or patterns of DNA sequence repeats. The resulting map provides important information about the organization and structure of the genome, and can be used for a variety of purposes, including identifying the location of genes associated with genetic diseases, studying evolutionary relationships between organisms, and developing genetic markers for use in breeding or forensic applications.

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- ... A single-site nanozyme was developed for tumor therapy. A SOD-like nanozyme was developed to regulate the mitochondria and ... The substrate is activated in a small part of the enzyme's macromolecule called the active site. There, the binding of a ...
This mutation interrupts a site of RNA splicing. The gene encodes a protein-acid alpha-glucosidase (EC is a ... The coding sequence of the putative catalytic site domain is interrupted in the middle by an intron of 101 bp. The promoter has ... LOTS was a randomized, double-blind, placebo-controlled study that enrolled 90 patients at eight primary sites in the United ... Inborn errors of carbohydrate metabolism Lysosomal storage disease Metabolic myopathies Pompe disease at NLM Genetics Home ...
"Transcription-coupled RNA surveillance in human genetic diseases caused by splice site mutations". Human Molecular Genetics. 24 ... Each hexamer of DNA base pairs has a positional distribution near splice sites where it is most likely to occur. Point ... Numerous sources cite that approximately one-third of disease-causing mutations affect RNA splicing. Such mutations frequently ... "Spliceman-a computational web server that predicts sequence variations in pre-mRNA splicing" (PDF). Bioinformatics. 28 (7): ...
Splice Site RNA Sequence". Biochemistry. 55 (18): 2553-66. doi:10.1021/acs.biochem.5b01240. PMID 27064654. Basu A, Dong B, ... Kameoka S, Duque P, Konarska MM (April 2004). "p54(nrb) associates with the 5' splice site within large transcription/splicing ... "Splicing and transcription-associated proteins PSF and p54nrb/nonO bind to the RNA polymerase II CTD". RNA. 8 (9): 1102-11. doi ... Straub T, Grue P, Uhse A, Lisby M, Knudsen BR, Tange TO, Westergaard O, Boege F (October 1998). "The RNA-splicing factor PSF/ ...
Chabot B, Black DL, LeMaster DM, Steitz JA (1986). "The 3' splice site of pre-messenger RNA is recognized by a small nuclear ... 1977). "Human beta-globin messenger RNA. I. Nucleotide sequences derived from complementary RNA". J. Biol. Chem. 252 (14): 5019 ... Ruskin B, Greene JM, Green MR (1985). "Cryptic branch point activation allows accurate in vitro splicing of human beta-globin ... van Santen VL, Spritz RA (1985). "mRNA precursor splicing in vivo: sequence requirements determined by deletion analysis of an ...
In addition, it has been suggested that RNA secondary structure prediction helps splice site prediction. Artificial neural ... The first is a smaller classifier, identifying donor splice sites and acceptor splice sites as well as start and stop codons. ... each position is a score based on whether the network thinks the window contains a donor splice site or an acceptor splice site ... "Impact of RNA structure on the prediction of donor and acceptor splice sites". BMC Bioinformatics. 7: 297. doi:10.1186/1471- ...
Siddique Z, McPhaden AR, Lappin DF, Whaley K (December 1991). "An RNA splice site mutation in the C1-inhibitor gene causes type ... Skriver K, Radziejewska E, Silbermann JA, Donaldson VH, Bock SC (February 1989). "CpG mutations in the reactive site of human ... deletion of Lys-251 results in acquisition of an N-glycosylation site". Proceedings of the National Academy of Sciences of the ... "Type I C1 inhibitor deficiency with a small messenger RNA resulting from deletion of one exon". The Journal of Clinical ...
Chua K, Reed R (2000). "The RNA splicing factor hSlu7 is required for correct 3' splice-site choice". Nature. 402 (6758): 207- ... 2008). "Regulation of transcription of the RNA splicing factor hSlu7 by Elk-1 and Sp1 affects alternative splicing". RNA. 13 ( ... Pre-mRNA-splicing factor SLU7 is a protein that in humans is encoded by the SLU7 gene. Pre-mRNA splicing occurs in two ... "Human step II splicing factor hSlu7 functions in restructuring the spliceosome between the catalytic steps of splicing". Genes ...
2001). "Structural basis for recognition of the intron branch site RNA by splicing factor 1". Science. 294 (5544): 1098-102. ... Arning S, Grüter P, Bilbe G, Krämer A (1996). "Mammalian splicing factor SF1 is encoded by variant cDNAs and binds to RNA". RNA ... 2001). "The transcription elongation factor CA150 interacts with RNA polymerase II and the pre-mRNA splicing factor SF1". Mol. ... "Entrez Gene: SF1 splicing factor 1". Rino J, Desterro JM, Pacheco TR, Gadella TW, Carmo-Fonseca M (May 2008). "Splicing factors ...
RNA-Seq) using Bowtie first and then mapping to a reference genome to discover RNA splice sites de novo. TopHat aligns RNA-Seq ... spliced alignment of RNA-Seq reads). Bowtie (sequence analysis) List of RNA-Seq bioinformatics tools Microarray analysis ... It is useful because it does not need to rely on known splice sites. TopHat can be used with the Tuxedo pipeline, and is ... Another advantage for TopHat is that it does not need to rely on known splice sites when aligning reads to a reference genome. ...
A point mutation near a gene may also create an alternative RNA splice site, resulting in a different transcript. By now, ... The 3' UTR, especially the poly(A) tail, plays a vital role in RNA processing, including maintenance of RNA stability and ... "Mechanism of alternative splicing and its regulation". Biomedical Reports. 3 (2): 152-158. doi:10.3892/br.2014.407. ISSN 2049- ... "Next-gen sequencing identifies non-coding variation disrupting miRNA-binding sites in neurological disorders". Molecular ...
Protein coding RNAs in mitochondria are spliced and edited using organelle-specific splice and editing sites. Nuclear copies of ... Any subsequent nuclear gene transfer would therefore also lack mitochondrial splice sites. The bulk flow hypothesis is the ... If the edited mitochondrial sequence recombines with the mitochondrial genome, mitochondrial splice sites would no longer exist ... do not contain organelle-specific splice sites, suggesting a processed mRNA intermediate. The cDNA hypothesis has since been ...
Furthermore, an alternative RNA splicing site is created leading to a loss of the quinone binding site. The variant protein of ... Gasdaska PY, Fisher H, Powis G (1995). "An alternatively spliced form of NQO1 (DT-diaphorase) messenger RNA lacking the ... Role of AP1 binding site contained within human antioxidant response element". J. Biol. Chem. 267 (21): 15097-104. doi:10.1016/ ... putative quinone substrate binding site is present in human normal and tumor tissues". Cancer Res. 55 (12): 2542-7. PMID ...
The carboxy-terminal domain is also the binding site for spliceosome factors that are part of RNA splicing. These allow for the ... RNA Pol II matches complementary RNA nucleotides to the template DNA by Watson-Crick base pairing. These RNA nucleotides are ... the capping of the RNA transcript, and attachment to the spliceosome for RNA splicing. The CTD typically consists of up to 52 ... The N-terminal domain of TFIIB brings the DNA into proper position for entry into the active site of RNA polymerase II. TFIIB ...
... alternative RNA splicing, and alternative translation start sites". J. Biol. Chem. 281 (11): 7282-93. doi:10.1074/jbc. ... Katoh M, Kirikoshi H, Saitoh T, Sagara N, Koike J (Sep 2000). "Alternative splicing of the WNT-2B/WNT-13 gene". Biochem Biophys ... This gene encodes a member of the wingless-type MMTV integration site (WNT) family of highly conserved, secreted signaling ... "Entrez Gene: WNT2B wingless-type MMTV integration site family, member 2B". Katoh M (2006). "WNT2B: comparative integromics and ...
The spliceosome is a large ribonucleoprotein which cleaves the RNA at the splicing site and recombines the exons of the RNA. ... RNA splicing removes the non-coding RNA introns leaving behind the exons, which are then spliced and joined together to form ... Mature messenger RNA, often abbreviated as mature mRNA is a eukaryotic RNA transcript that has been spliced and processed and ... See RNA Splicing for further details. Alberts, Bruce (2015). Molecular biology of the cell (Sixth ed.). Abingdon, UK: Garland ...
Pseudoknots are commonly found in viral genomes, especially RNA viruses, where they incorporate an RNA splice site and can have ... splice site pseudoknot/hairpin family". RNA Biology. 9 (11): 1305-1310. doi:10.4161/rna.22343. PMC 3597570. PMID 23064116. ... Moss WN, Dela-Moss LI, Kierzek E, Kierzek R, Priore SF, Turner DH (March 2012). Lewin A (ed.). "The 3′ Splice Site of Influenza ... Another pseudoknot occurs at the Influenza A Segment 7 Splice Site, which is used to produce the important viral M2 ion channel ...
Stahley, MR; Strobel SA (2006). "RNA splicing: group I intron crystal structures reveal the basis of splice site selection and ... Intron Group I Intron Sequence and Structure Database Splice site Nuclear introns Group II intron Group III intron Twintron ... splice site located in P1, resulting in a free 3'-OH group at the upstream exon and the exoG being attached to the 5' end of ... splice site in P10, leading to the ligation of the adjacent upstream and downstream exons and release of the catalytic intron. ...
A mutation introduces a cryptic splice site that is used instead of the wild-type splice site during post-transcriptional RNA ... to a segment of the 216 G to A mutant mRNA and mechanically blocks the cryptic splice site so that the wild type splice site is ... The consequent mis-splicing causes the 35-nucleotide deletion in the mature mRNA transcript. Since the change in the RNA ... Lentz J, Savas S, Ng SS, Athas G, Deininger P, Keats B (February 2005). "The USH1C 216G-->A splice-site mutation results in a ...
These tags are then amplified by PCR with primers containing a mismatch changing the Bpm1 site to a Xho1 site. The amplicons ... 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 ...
1988) describes in his studies that sequence with RNA splice sites are preserved in SERPINA2, and when expressed, it encodes a ...
Rail-RNA Scalable analysis of RNA-seq splicing and coverage. RAP RNA-Seq Analysis Pipeline, a new cloud-based NGS web ... Rail-RNA Scalable analysis of RNA-seq splicing and coverage. RPASuite RPASuite (RNA Processing Analysis Suite) is a ... RNA-Skim RNA-Skim: a rapid method for RNA-Seq quantification at transcript-level. rSeq rSeq is a set of tools for RNA-Seq data ... RASER: reads aligner for SNPs and editing sites of RNA. SeqSaw SoapSplice A tool for genome-wide ab initio detection of splice ...
The repressive function of Human MBNL1 by sequestering at normal splice sites has been shown to lead to RNA-splicing defects ... Muscleblind Like Splicing Regulator 1 (MBNL1) is an RNA splicing protein that in humans is encoded by the MBNL1 gene. It has a ... Teplova M, Patel DJ (December 2008). "Structural insights into RNA recognition by the alternative-splicing regulator ... "Colocalization of muscleblind with RNA foci is separable from mis-regulation of alternative splicing in myotonic dystrophy". ...
She discovered spliceosomes, the particles that are the sites of splicing of pre-messenger RNA into the final mature mRNA and ... A snRNP is a specific short length of RNA, around 150 nucleotides long, associated with protein, that is involved in splicing ... Her work helps explain the phenomenon of "alternative RNA splicing." Her discovery of the snRNPs and snoRNPs explains a ... "RNA Interviews: Dr. Joan Steitz", Ambion TechNotes v. 10, n. 1 (March 2003) (available at ...
The major spliceosome splices introns containing GU at the 5' splice site and AG at the 3' splice site. It is composed of the ... splice site of an intron; Splicing factor 1 binds to the intron branch point sequence; U2AF1 binds at the 3' splice site of the ... in HIV-1 there are many donor and acceptor splice sites. Among the various splice sites, ssA7, which is 3' acceptor site, folds ... Several methods of RNA splicing occur in nature; the type of splicing depends on the structure of the spliced intron and the ...
... splice site in two distinct stages during the second catalytic step of pre-mRNA splicing". RNA. 1 (6): 584-97. PMC 1369303. ... splice site is recognized by p220 of the U5 snRNP within the spliceosome". RNA. 2 (3): 213-25. PMC 1369364. PMID 8608445. Hinz ... splice site". RNA. 5 (2): 167-79. doi:10.1017/S1355838299981785. PMC 1369749. PMID 10024169. Makarov EM, Makarova OV, Achsel T ... Chiara MD, Palandjian L, Feld Kramer R, Reed R (Aug 1997). "Evidence that U5 snRNP recognizes the 3' splice site for catalytic ...
... and SRp40 on the utilization of the A1 to A5 splicing sites of HIV-1 RNA". The Journal of Biological Chemistry. 279 (29): 29963 ... Serine/arginine-rich splicing factor 7 (SRSF7) also known as splicing factor, arginine/serine-rich 7 (SFRS7) or splicing factor ... Jacquenet S, Decimo D, Muriaux D, Darlix JL (2006). "Dual effect of the SR proteins ASF/SF2, SC35 and 9G8 on HIV-1 RNA splicing ... Each of these factors contains an RNA recognition motif (RRM) for binding RNA and an RS domain for binding other proteins. The ...
... and SRp40 on the utilization of the A1 to A5 splicing sites of HIV-1 RNA". The Journal of Biological Chemistry. 279 (29): 29963 ... Splicing factor, arginine/serine-rich 5 is a protein that in humans is encoded by the SFRS5 gene. GRCh38: Ensembl release 89: ... "Entrez Gene: SFRS5 splicing factor, arginine/serine-rich 5". Zahler AM, Lane WS, Stolk JA, Roth MB (May 1992). "SR proteins: a ... Du K, Taub R (December 1997). "Alternative splicing and structure of the human and mouse SFRS5/HRS/SRp40 genes". Gene. 204 (1-2 ...
... rna 3' polyadenylation signals MeSH G14.340.024.340.137.780 - rna splice sites MeSH G14.340.024.340.137.785 - rna 5' terminal ... rna 3' polyadenylation signals MeSH G14.080.689.687.490 - rna splice sites MeSH G14.080.689.687.500 - rna 5' terminal ... chromosome fragile sites MeSH G14.340.024.220 - dna, intergenic MeSH G14.340.024.220.150 - dna, satellite MeSH G14.340.024.220. ... attachment sites, microbiological MeSH G14.340.024.159 - cpg islands MeSH G14.340.024.189 - dna sequence, unstable MeSH G14.340 ...
... rna 3' polyadenylation signals MeSH G06.184.603.080.689.687.490 - rna splice sites MeSH G06.184.603.080.689.687.500 - rna 5' ... rna editing MeSH G06.535.839.700 - rna splicing MeSH G06.535.839.700.100 - alternative splicing MeSH G06.535.839.700.750 - ... protein splicing MeSH G06.535.770.871.850 - transfer rna aminoacylation MeSH G06.535.780.101 - area under curve MeSH G06.535. ... MeSH G06.184.154.147 - allosteric site MeSH G06.184.154.290 - bay region (chemistry) MeSH G06.184.154.309 - binding, ...
RNA (5-R(*GP*GP*AP*GP*UP*AP*AP*GP*UP*CP*U)-3)2-(8-fluoranyl-2-methyl-imidazo[1,2-a]pyridin-6-yl)-7-(4-methylpiperazin-1-yl) ... RNA (5-R(*AP*UP*AP*CP*(PSU)P*(PSU)P*AP*CP*CP*UP*G)-3) ... splice site of SMN2 exon7 in complex with the SMN-C5 splicing ... RNA (5-r(*ap*up*ap*cp*(psu)p*(psu)p*ap*cp*cp*up*g)-3) ... RNA (5-r(*gp*gp*ap*gp*up*ap*ap*gp*up*cp*u)-3) ... 6HMO: Solution structure of the RNA duplex formed by the 5-end of U1snRNA and the 5- ...
... when coupled with splicing, have variable coding sequences. APA is an important layer of gene expression program critical for ... RNA Splice Sites * RNA Splicing* * RNA, Messenger * mRNA Cleavage and Polyadenylation Factors ... For intronic polyadenylation (IPA), splicing features, such as strengths of 5 splice site and 3 splice site, also affect ... Here, by using a catalytically dead Cas9 and coupling its target site with polyadenylation site (PAS), we develop a method, ...
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- ... A single-site nanozyme was developed for tumor therapy. A SOD-like nanozyme was developed to regulate the mitochondria and ... The substrate is activated in a small part of the enzymes macromolecule called the active site. There, the binding of a ...
Alternative Splicing Video. However in few cases, video content could be different than the title. ... Alternative Splicing This Scientific content most probably shows video related to topic: ... RNA Splicing. 01:39 , 11002 views Watch VIDEO. 15356 views mRNA Splicing. 01:39 , 15356 views ...
Self-splicing of group II introns in vitro: lariat formation and 3 splice site selection in mutant RNAs. Schmelzer, C., Müller ... Using homology modeling and site-directed mutagenesis, we have localized the RNA-binding surface of the Smaug SAM domain and ... splice site [18].. *The transcription factor GATA-1 is a fundamental regulator of genes in haematopoietic cell lineages and ... The RNA-binding SAM domain of Smaug defines a new family of post-transcriptional regulators. Aviv, T., Lin, Z., Lau, S., Rendl ...
Putative NS and VP1/VP2 gene RNA splicing sites were detected in the GFADV genome, which suggests the expression of different ... Potential RNA splicing signals in AMDV were present on the GFADV genome (Technical Appendix Figure 1) (4). The predicted ... Alternative splicing enables expression of multiple messenger RNAs (4). AMDV strains can exhibit sequence variability in their ... Skip directly to site content Skip directly to page options Skip directly to A-Z link Skip directly to A-Z link Skip directly ...
"A second leaky splice-site mutation in the spastin gene." Am J Hum Genet, vol. 69, no. 6, Dec. 2001, pp. 1407-09. Pubmed, doi: ... A second leaky splice-site mutation in the spastin gene.. Publication , Journal Article ... A second leaky splice-site mutation in the spastin gene. Am J Hum Genet. 2001 Dec;69(6):1407-9. ... A second leaky splice-site mutation in the spastin gene. Am J Hum Genet. 2001 Dec;69(6):1407-1409. ...
RNA Splice Sites - Preferred Concept UI. M0359363. Scope note. Nucleotide sequences located at the ends of EXONS and recognized ... 5 Splice Site 5 Splice Sites Donor Site, Splice Donor Sites, Splice Splice Donor Sites Splice Site, 5 Splice Sites, 5 ... 3 Splice Site 3 Splice Sites Acceptor Site, Splice Acceptor Sites, Splice Splice Acceptor Sites Splice Site, 3 Splice Sites ... Splice Acceptor Site. Splice Acceptor Sites. Splice Donor Site. Splice Donor Sites. Splice Site, 3. Splice Site, 5. Splice ...
RNA Splice Sites Medicine & Life Sciences 18% * Binding Sites Medicine & Life Sciences 11% ... We identified a binding site for the splicing regulatory protein hnRNP A1 downstream of the IKBKAP exon 20 5-splice site. We ... We identified a binding site for the splicing regulatory protein hnRNP A1 downstream of the IKBKAP exon 20 5-splice site. We ... We identified a binding site for the splicing regulatory protein hnRNP A1 downstream of the IKBKAP exon 20 5-splice site. We ...
... splice site and alternative 5 splice site usage, which were about 50 to 100% higher in the liver than in any other human ... possibly contributing to the unusually high frequency of alternative splice site usage seen in liver. Sequence motifs enriched ... Quantifying differences in splice junction usage, the brain, pancreas, liver and the peripheral nervous system had the most ... To compare AS events across human tissues, we analyzed the splicing patterns of genomically aligned expressed sequence tags ( ...
RNA Splice Sites. *Zinc Finger E-box-Binding Homeobox 1. *Drug Resistance ... Home] Page last revised: 31 August, 2019 Cancer Genetics Web, Established 1999 ... Disclaimer: This site is for educational purposes only; it can not be used in diagnosis or treatment. ... In our RNA sequencing study on gastric cancer patients, Runt-related transcription factor-3 (RUNX3) expression was ...
Messenger RNA 33% * Lung Diseases 26% * Meconium Ileus 23% * RNA Splice Sites 18% ... All content on this site: Copyright © 2024 Elsevier B.V. or its licensors and contributors. All rights are reserved, including ...
... splice site selection. It has been shown that different CCCH-type Znf proteins interact with the 3-untranslated region of ... role in both constitutive and enhancer-dependent splicing by mediating essential protein-protein interactions and protein-RNA ... The mutant peptide unexpectedly showed loss of one of its metal binding sites and displayed ordered structure for only the ... Another protein containing this domain is the human splicing factor U2AF 35kDa subunit, which plays a critical ...
... complex containing RNA products from the 1st step of splicing to form catalytic site for the second step of splicing. View ... Pre-mRNA intron-binding component of the U4/U6 x U5 tri-snRNP complex; involved in mRNA 3- and 5-splice site recognition and ... Component of U4/U6-U5 snRNP complex; involved in second catalytic step of splicing; participates in spliceosomal assembly ... broad splicing defect. Classical Genetics. conditional. *heat sensitivity: increased ...
Splicing at the second alternative site (exon 9) is thought to have a great biological importance and results in the inclusion ... 2, 3, 4, 5] The WT1 gene contains 10 exons that produce 4 different messenger RNAs (mRNAs) as a result of 2 alternative ... Mutations that disrupt the second alternative splicing site of the WT1 gene alter the normal ratio of KTS-positive/negative ... All material on this website is protected by copyright, Copyright © 1994-2023 by WebMD LLC. This website also contains material ...
... inducing a spliceopathy that leads to a developmental remodelling of the transcriptome due to an adult-to-foetal splicing ... are two families of tissue-specific regulators of developmentally programmed alternative splicing that act as antagonist ... describing the molecular mechanisms underlying alternative splicing misregulation for a deeper understanding of DM1 complexity ... MBNL splicing activity depends on RNA binding site structural context. Nucleic Acids Res. 2018, 46, 9119-9133. [Google Scholar ...
... and necessary information processing sites, such as ribosome binding sites, RNA splice sites, polyadenylation sites, and ... Similar creation of additional restriction sites by nucleotide substitutions at the disclosed mutation sites can be readily ... For example, such polynucleotides can include a promoter, a transcription termination site (polyadenylation site in eukaryotic ... and the sequence TTTGAT 90 bp upstream of the translational start site resembles the -10 consensus promoter site, followed by ...
RNA Splice Sites. *RNA Splicing. *RNA, Messenger. *Salpingostomy. *Selection, Genetic. *Selective Estrogen Receptor Modulators ...
... create an aberrant donor splice site Feature rna; 2 Feature /dnalink: 1 Feature /aalink: 3 Feature /name: loss of exon sequence ... splice site and leading to 22 bp deletion from exon 1, Description frameshift and stop codon in SH2 domain Date 03-Oct-2001 ( ... splice site Date 10-Jun-1999 (Rel. 1, Created) Date 10-Jun-1999 (Rel. 1, Last updated, Version 1) RefNumber [1] RefCrossRef ... splice site Date 10-Jun-1999 (Rel. 1, Created) Date 10-Jun-1999 (Rel. 1, Last updated, Version 1) RefNumber [1] RefCrossRef ...
Identification of novel point mutations in splicing sites integrating whole-exome and RNA-seq data in myeloproliferative ... Identification of novel point mutations in splicing sites integrating whole-exome and RNA-seq data in myeloproliferative ... of a Novel Splicing Mutation in Blast Crisis Transformation of Chronic Myeloid Leukemia Integrating Whole-exome and RNA-Seq ... of a Novel Splicing Mutation in Blast Crisis Transformation of Chronic Myeloid Leukemia Integrating Whole-exome and RNA-Seq ...
RNA sequencing complemented WES when multiple potentially pathogenic splice-site mutations were found. ... non-invasive and efficient RNA therapy to correct mutations within COL7A1 via spliceosome-mediated RNA trans-splicing (SMaRT). ... COL7A1 Editing via RNA Trans-Splicing in RDEB-Derived Skin Equivalents. Liemberger, Bernadette; Bischof, Johannes; Ablinger, ... of novel splice-site mutations was determined through reverse transcriptase-PCR of skin mRNA followed by Sanger and/or RNA ...
You are here: Home / Expert view / GEP fellow publishes RNA splicing study ... GEP fellow publishes RNA splicing study 29th October 2021. /in Expert view, Research /Tags: Genomic testing, Rare inherited ... Essential Website Cookies. These cookies are strictly necessary to provide you with services available through our website and ... This site uses cookies. By continuing to browse the site, you are agreeing to our use of cookies. ...
RNA sequencing and conditional Nova mutants reveal that Nova protein function is necessary for activity-dependent alternative ... splicing of synaptic genes within somatostatin cortical interneurons and regulates its afferent and efferent connectivity. ... 2005) CLIP: A method for identifying protein-RNA interaction sites in living cells Methods 37:376-386. ... splice site, A5, alternative 3 splice site, A3 (right). (B) Histogram of the magnitude of activity-dependent splicing changes ...
RNA-Seq • 1.9k views ADD COMMENT • link 5.5 years ago by solo7773 ▴ 90 ... I Googled but failed to find out how to define the 5 prime splice sites and then write them into a bed file, or where to ... I just want to ask how can I get coordinates around 3 splice site instead TSS so what can I use instead of the promoters for ... Im reading an article in which there is a figure showing how many reads there are around the 5 prime splice site. I want to ...
Splice site m6A methylation prevents binding of U2AF35 to inhibit RNA splicing. Cell. 2021 Jun 10;184(12):3125-3142.e25. ► ... Parent site Institute of Genetics and Genomics in Geneva - iGE3 Institute of Genetics and Genomics in Geneva - iGE3 *Home ... throughput screening identifies SOX2 as a super pioneer factor that inhibits DNA methylation maintenance at its binding sites. ...
Splicing at the second alternative site (exon 9) is thought to have a great biological importance and results in the inclusion ... 2, 3, 4, 5] The WT1 gene contains 10 exons that produce 4 different messenger RNAs (mRNAs) as a result of 2 alternative ... Mutations that disrupt the second alternative splicing site of the WT1 gene alter the normal ratio of KTS-positive/negative ... All material on this website is protected by copyright, Copyright © 1994-2023 by WebMD LLC. This website also contains material ...
We evaluated WAMs in the context of splice site prediction and CMs in the context of predicting RNA or other genomic elements ... Acceptor splice site dataset for P. falciparum. We have extracted 7582 acceptor splice sites from PlasmoDB release 6.4. This ... Splice sites were used for three reasons: first, splice site prediction is at the heart of gene prediction, an biologically ... The second part, having 6582 acceptor splice sites, was used as positive testing set. Each acceptor splice site sequence has 70 ...
  • Splicing at the second alternative site (exon 9) is thought to have a great biological importance and results in the inclusion or exclusion of 3 amino acids, lysine, threonine, and serine (KTS), yielding the KTS-positive isoform when the amino acids are included and KTS-negative isoform when excluded. (
  • The human, paired guide Poison (pgPoison) library targets 3` splice sites with paired guide RNAs for alternative exon removal (pgRNAs), induce skipping of 'poison' cassette exons and corresponding upstream constitutive exons in ultraconserved regions. (
  • One form of the disease, LCA10 is caused by an intronic mutation in CEP290 that causes a defective splice site and inserts an exon that does not belong in the mRNA, resulting in a premature termination codon (3). (
  • Sepofarsen is an ASO that binds to the defective splice site, excluding exon X, and restoring correct splicing. (
  • 2 − 6 These nuclease-resistant polymers persist in live organisms for days and are typically designed to recognize 25-base sequences that span intron-exon junctions or translational start sites. (
  • In SMN2, this splicing event results in the exclusion of exon 7 from most of its mRNA molecules, leading to the generation of a shorter, less stable, and poorly working survival motor neuron protein. (
  • In our projects, we combine physiological measurements like VO2max, muscular strength, and glucose tolerance with preclinical readouts, for example RNA and ChIP sequencing, fibre typing, gene knockdown, and exon skipping. (
  • 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. (
  • As a quick reminder, a gene may have many forms (isoforms) depending on which exons and transcription start sites are used for transcription. (
  • The alternative splicing events it can detect include: (1) skipped exons, (2) 5′ and 3′ alternative splice site usage, and (3) additional complex events that can be summarized by differences in intron excision / inclusion. (
  • This method employs capture probes that target known exons, allowing for the enrichment of coding RNAs. (
  • In this case, pieces of genetic information - exons - can change the resulting messenger RNA (mRNA) and final protein. (
  • These experiments will show how a Ca ++ signal changes the phosphorylation status of splicing regulatory proteins and which genes are affected by this regulation. (
  • We show that ALS heritability is enriched in splicing variants and in binding sites of 6 RNA-binding proteins including TDP-43 and FUS. (
  • This work highlighted core splicing proteins, including SF3B1, frequently mutated in various cancers. (
  • Alternative splicing is a natural process that allows for a single gene to give rise to many different proteins, adding or removing certain key ingredients. (
  • Mutations that disrupt the second alternative splicing site of the WT1 gene alter the normal ratio of KTS-positive/negative isoforms from 2:1 to 1:2 and result in abnormalities in glomerular formation and gonadal differentiation seen in Frasier syndrome. (
  • Splicing factor mutations are particularly prevalent in MDS, a group of heterogeneous hematological disorders characterized by defective blood stem cells and a high risk of leukemia development. (
  • Accumulating evidence is highlighting a role for aberrant splicing in cancer even in the absence of splicing factors mutations. (
  • We are analysing alternative splicing and its association with germline variants and somatic mutations RNA and DNA sequencing data for thousands of women with sporadic or familial breast cancer. (
  • This method allows for simultaneous quantification of a multitude of RNA transcripts, enabling unbiased annotation of splicing variants, novel transcripts, and non-coding RNAs. (
  • Our aims are to understand how variants in regulatory motifs control alternative splicing and intron retention and to use this information to develop accurate methods for identification of functional variants. (
  • The overwhelming majority of full-length and truncated elements (82/86 and 40/49, respectively) contained one or two specific motifs required for binding of the VL30 RNA to the poly-pyrimidine tract-binding protein-associated splicing factor (PSF). (
  • In aim 2 , the target genes of the splicing factors will be determined by cross-linking and immunoprecipitation (CLIP) and compared with the CLIP results obtained from phosphorylated splicing factors. (
  • Putative target genes identified by CLIP, preferentially ion channels will be cloned in frame with GFP reporters, resulting in splice site selection dependent GFP expression. (
  • In aim 3 , we will use these systems to manipulate Ca ++ levels and determine their effect on tra2-beta, AChE-R and trk-B splice site selection, as well as on genes identified in WP1. (
  • In participating UK research institutions, investigators can publish open access in Genome Research, Genes & Development, RNA, and Learning & Memory without article publication charges and all staff can read the entire renowned Cold Spring Harbor journal collection. (
  • Additionally, we investigated the gene expression measurement in comparison to the TaqMan standard data and assessed the detection of fusion genes engineered in the FFPE reference RNA. (
  • Most VL30 sequences were found integrated either near, adjacent or inside transcription start sites, or into introns or at the 3' end of genes. (
  • Although Basepair offers pipelines for isoform-level quantification, this new pipeline uses LeafCutter, a new, state-of-the-art tool for detecting splicing changes. (
  • Annotation-free quantification of RNA splicing using LeafCutter. (
  • Alternative splicing enables expression of multiple messenger RNAs ( 4 ). (
  • the influence of trkB-T1-activity dependent Ca ++ fluctuations on alternative splicing. (
  • We are pleased to announce the release of our new pipeline for investigating changes in alternative splicing (AS) in RNA-seq. (
  • Another gene, SMN2, which has a slight difference in its DNA sequence, results in alternative splicing and limits the amount of working survival motor neuron it produces by 10 to 15 percent. (
  • Long noncoding RNA ABHD11-AS1 interacts with SART3 and regulates CD44 RNA alternative splicing to promote lung carcinogenesis. (
  • The RNA splicing pipeline uses reads mapping to the intron to statistically test for significant differences in novel and known AS events between two sample groups. (
  • PSI stands for Percentage Spliced In, which is defined as the average proportion of transcripts that contain a given intron in the sample group. (
  • RNA splicing is a major nexus of gene expression regulation, shaping cellular identity during development, frequently altered in human cancers. (
  • The frameshifting RNA element (FSE) in coronaviruses (CoVs) regulates the programmed -1 ribosomal frameshift (-1 PRF) mechanism common to many viruses. (
  • Researchers at Lund University Faculty of Medicine have determined a novel mechanism linking the metabolism of ribonucleic acids, RNA, to the development of leukemia in myelodysplastic syndrome patients, MDS. (
  • A team of researchers led by Dr. Cristian Bellodi recently discovered a hardwired genetic control mechanism modulating individual spliceosomal components, known as splicing factors, in cells harboring oncogenic lesions common in human cancers. (
  • Cold Spring Harbor, NY -- Cold Spring Harbor Laboratory Press announced the release of Genetic Counseling: Clinical Practice and Ethical Considerations, available on its website in Hardcover and Paperback formats. (
  • Nusinersen binds to SMN2's mRNA molecule and corrects its splicing. (
  • There is great potential to fully assess the performance characteristics, including accuracy, reproducibility, and analytical sensitivity, of RNA-Seq for detecting the fusion events. (
  • RNA-Seq analysis of Formalin-Fixed and Paraffin-Embedded (FFPE) samples has emerged as a highly effective approach and is increasingly being used in clinical research and drug development. (
  • However, the processing and storage of FFPE samples are known to cause extensive degradation of RNAs, which limits the discovery of gene expression or gene fusion-based biomarkers using RNA sequencing, particularly methods reliant on Poly(A) enrichment. (
  • To address this gap, we designed the study to evaluate the performance of three exome capture-based library preparation kits on human reference RNA from the Sequencing Quality Control consortium [ 6 ] and commercially available FFPE sections (Fig. 1 ). (
  • I'm reading an article in which there is a figure showing how many reads there are around the 5 prime splice site. (
  • This hyperphosphorylation is caused by unknown Ca ++ -dependent kinases after an increase in the intracellular calcium concentration and results in a change of splice site selection and the cytosolic accumulation of normally nuclear splicing factors. (
  • The hyperphosphorylation and cytosolic accumulation of EGFP-tagged splicing factors will be determined by PAGE and real-time fluorescent microscopy (WP5), respectively. (
  • Once the kinase is identified, GFP-tagged versions of splicing factors will be expressed in cells, isolated by immunoprecipitation and the phosphorylation sites will be determined by mass-spectroscopy (WP4). (
  • However, little is known about the contribution of the non-mutated splicing factors in tumor evolution," explain the researchers. (
  • Particular interest is devoted to the study of splicing factors and their role in the onset and progression of cancer. (
  • This approach involves the intramolecular cross-linking of 5′ amine- and 3′ disulfide-modified MO oligonucleotides using appropriately functionalized tethers, generating macrocyclic structures that conformationally resist RNA hybridization. (
  • To investigate the FSE structural evolution, we use our graph theory-based methods for representing RNA secondary structures in the RNA-As-Graphs (RAG) framework to calculate conformational landscapes of viral FSEs with increasing sequence lengths for representative 10 Alpha and 13 Beta-CoVs. (
  • RNA sequencing has been developed as one of the most sensitive tools for gene expression analysis. (
  • Analysis of LTRs revealed a high number of common transcription factor binding sites, possibly explaining the known inducible and tissue-specific expression of individual elements. (
  • Available RNA sequencing data from the Genotype-Tissue Expression (GTEx) project revealed a surprisingly high expression level for the short isoform of about half the level of the canonical isoform in human kidney tissue (Fig. 1 a). (
  • Chronic hexavalent chromium exposure upregulates the RNA methyltransferase METTL3 expression to promote cell transformation, cancer stem cell-like property, and tumorigenesis. (
  • Cold Spring Harbor, NY -- Cold Spring Harbor Laboratory Press (CSHLP) announced the release of Metastasis: Mechanism to Therapy, available on its website in Hardcover format. (
  • Columbia faculty along with investigators from three other sites participated in the initial, first-in-human phase 1/2 trials with nusinersen, with Columbia dosing the first ever patient with nusinersen in December 2011. (
  • Public health officials and others concerned with appropriate actions to take at hazardous waste sites may want information on levels of exposure associated with more subtle effects in humans or animals (LOAELs) or exposure levels below which no adverse effects (NOAELs) have been observed. (
  • Recently, researchers have developed an exome targeted RNA-Seq methodology that utilizes biotinylated oligonucleotide probes to enrich RNA transcripts of interest, which could overcome these limitations. (
  • I Googled but failed to find out how to define the 5 prime splice sites and then write them into a bed file, or where to download this sort of data from a public available data base. (
  • Cold Spring Harbor, NY -- Cold Spring Harbor Laboratory Press (CSHLP) announced the release of The Digital Cell: Cell Biology as a Data Science, available on its website in hardcover format. (
  • The results aim to provide the scientific community with a comprehensive assessment of exome capture methods for RNA sequencing of FFPE samples. (
  • To learn more about targeting RNA splicing, see this article . (
  • Journal Article] What is the switch for coupling transcription and splicing? (
  • How to plot a profile showing read coverage around the 5 prime splice site? (
  • We and others have synthesized light-activatable cMOs that allow spatiotemporal control of RNA splicing or translation, complementing the use of conditional knockouts to study stage- and tissue-specific differences in gene function. (
  • Following these investigations, the CHERISH trial, a phase 3 randomized study, was launched at 24 sites to evaluate nusinersen's safety and effectiveness in children ages 2 to 12 with SMA types 2 and 3, who were able to sit, but not walk, independently. (
  • NewYork-Presbyterian Morgan Stanley Children's Hospital served as one of the study sites led by Claudia A. Chiriboga, MD , a child neurologist and Professor of Neurology and Pediatrics at Columbia and a member of Columbia's Motor Neuron Center. (
  • Among the library preparation methods, the standard Poly(A) enrichment protocol provides a comprehensive and accurate view of polyadenylated RNAs. (
  • Now what I know is that computeMatrix from deepTools can do this visualization once got the 5 splice sites region information. (
  • Please use a modern browser to fully experience our website, such as the newest versions of Edge, Chrome, Firefox or Safari etc. (
  • In a parallel approach, we will directly test minigenes generated in WP1 containing the tra2-beta1 binding site GHVVGANR for their tra2-beta1 dependence. (
  • Reduction of podocin levels at the site of the slit diaphragm complex has a detrimental effect on podocyte function and morphology. (
  • The substrate is activated in a small part of the enzyme's macromolecule called the active site. (
  • Nous avons génotypé les deux polymorphismes mononucléotidiques du gène ADIPOQ chez 140 patients atteints de DNID sans lien de parenté et 66 témoins non diabétiques en recourant à l'analyse du polymorphisme de longueur des fragments de restriction par réaction en chaîne de polymérase. (
  • Share sensitive information only on official, secure websites. (