RNA Splice Sites: 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.RNA Splicing: The ultimate exclusion of nonsense sequences or intervening sequences (introns) before the final RNA transcript is sent to the cytoplasm.Introns: Sequences of DNA in the genes that are located between the EXONS. They are transcribed along with the exons but are removed from the primary gene transcript by RNA SPLICING to leave mature RNA. Some introns code for separate genes.RNA Precursors: RNA transcripts of the DNA that are in some unfinished stage of post-transcriptional processing (RNA PROCESSING, POST-TRANSCRIPTIONAL) required for function. RNA precursors may undergo several steps of RNA SPLICING during which the phosphodiester bonds at exon-intron boundaries are cleaved and the introns are excised. Consequently a new bond is formed between the ends of the exons. Resulting mature RNAs can then be used; for example, mature mRNA (RNA, MESSENGER) is used as a template for protein production.Ribonucleoproteins, Small Nuclear: 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).Exons: 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.Alternative Splicing: A process whereby multiple RNA transcripts are generated from a single gene. Alternative splicing involves the splicing together of other possible sets of EXONS during the processing of some, but not all, transcripts of the gene. Thus a particular exon may be connected to any one of several alternative exons to form a mature RNA. The alternative forms of mature MESSENGER RNA produce PROTEIN ISOFORMS in which one part of the isoforms is common while the other parts are different.Base Sequence: The sequence of PURINES and PYRIMIDINES in nucleic acids and polynucleotides. It is also called nucleotide sequence.Molecular Sequence Data: Descriptions of specific amino acid, carbohydrate, or nucleotide sequences which have appeared in the published literature and/or are deposited in and maintained by databanks such as GENBANK, European Molecular Biology Laboratory (EMBL), National Biomedical Research Foundation (NBRF), or other sequence repositories.Ribonucleoproteins: Complexes of RNA-binding proteins with ribonucleic acids (RNA).Spliceosomes: 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.RNA, Small Nuclear: 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.Ribonucleoprotein, U1 Small Nuclear: 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.Amino Acid Sequence: The order of amino acids as they occur in a polypeptide chain. This is referred to as the primary structure of proteins. It is of fundamental importance in determining PROTEIN CONFORMATION.Mutation: 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.RNA, Messenger: RNA sequences that serve as templates for protein synthesis. Bacterial mRNAs are generally primary transcripts in that they do not require post-transcriptional processing. Eukaryotic mRNA is synthesized in the nucleus and must be exported to the cytoplasm for translation. Most eukaryotic mRNAs have a sequence of polyadenylic acid at the 3' end, referred to as the poly(A) tail. The function of this tail is not known for certain, but it may play a role in the export of mature mRNA from the nucleus as well as in helping stabilize some mRNA molecules by retarding their degradation in the cytoplasm.Ribonucleoprotein, U2 Small Nuclear: 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.Binding Sites: The parts of a macromolecule that directly participate in its specific combination with another molecule.HeLa Cells: 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.Consensus Sequence: A theoretical representative nucleotide or amino acid sequence in which each nucleotide or amino acid is the one which occurs most frequently at that site in the different sequences which occur in nature. The phrase also refers to an actual sequence which approximates the theoretical consensus. A known CONSERVED SEQUENCE set is represented by a consensus sequence. Commonly observed supersecondary protein structures (AMINO ACID MOTIFS) are often formed by conserved sequences.DNA Mutational Analysis: Biochemical identification of mutational changes in a nucleotide sequence.Sequence Homology, Nucleic Acid: 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.Nucleic Acid Conformation: The spatial arrangement of the atoms of a nucleic acid or polynucleotide that results in its characteristic 3-dimensional shape.Ribonucleoprotein, U5 Small Nuclear: 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.Transcription, Genetic: The biosynthesis of RNA carried out on a template of DNA. The biosynthesis of DNA from an RNA template is called REVERSE TRANSCRIPTION.Cloning, Molecular: 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-Binding Proteins: Proteins that bind to RNA molecules. Included here are RIBONUCLEOPROTEINS and other proteins whose function is to bind specifically to RNA.Polymerase Chain Reaction: In vitro method for producing large amounts of specific DNA or RNA fragments of defined length and sequence from small amounts of short oligonucleotide flanking sequences (primers). The essential steps include thermal denaturation of the double-stranded target molecules, annealing of the primers to their complementary sequences, and extension of the annealed primers by enzymatic synthesis with DNA polymerase. The reaction is efficient, specific, and extremely sensitive. Uses for the reaction include disease diagnosis, detection of difficult-to-isolate pathogens, mutation analysis, genetic testing, DNA sequencing, and analyzing evolutionary relationships.Protein Isoforms: Different forms of a protein that may be produced from different GENES, or from the same gene by ALTERNATIVE SPLICING.Sequence Analysis, DNA: A multistage process that includes cloning, physical mapping, subcloning, determination of the DNA SEQUENCE, and information analysis.Heterogeneous-Nuclear Ribonucleoprotein Group A-B: 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.Conserved Sequence: 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.Nuclear Proteins: 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.Sequence Alignment: The arrangement of two or more amino acid or base sequences from an organism or organisms in such a way as to align areas of the sequences sharing common properties. The degree of relatedness or homology between the sequences is predicted computationally or statistically based on weights assigned to the elements aligned between the sequences. This in turn can serve as a potential indicator of the genetic relatedness between the organisms.Heterogeneous-Nuclear Ribonucleoprotein Group F-H: A group of closely-related heterogeneous-nuclear ribonucleoproteins that are involved in pre-mRNA splicing.Ribonucleoprotein, U4-U6 Small Nuclear: 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.Nucleic Acid Precursors: Use for nucleic acid precursors in general or for which there is no specific heading.Isomerases: A class of enzymes that catalyze geometric or structural changes within a molecule to form a single product. The reactions do not involve a net change in the concentrations of compounds other than the substrate and the product.(from Dorland, 28th ed) EC 5.DNA, Complementary: 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.Models, Genetic: 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.Plasmids: 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.Cell Line: Established cell cultures that have the potential to propagate indefinitely.DNA: A deoxyribonucleotide polymer that is the primary genetic material of all cells. Eukaryotic and prokaryotic organisms normally contain DNA in a double-stranded state, yet several important biological processes transiently involve single-stranded regions. DNA, which consists of a polysugar-phosphate backbone possessing projections of purines (adenine and guanine) and pyrimidines (thymine and cytosine), forms a double helix that is held together by hydrogen bonds between these purines and pyrimidines (adenine to thymine and guanine to cytosine).Regulatory Sequences, Nucleic Acid: Nucleic acid sequences involved in regulating the expression of genes.Substrate Specificity: A characteristic feature of enzyme activity in relation to the kind of substrate on which the enzyme or catalytic molecule reacts.RNA, Viral: Ribonucleic acid that makes up the genetic material of viruses.Sequence Homology, Amino Acid: The degree of similarity between sequences of amino acids. This information is useful for the analyzing genetic relatedness of proteins and species.DNA Primers: 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.Point Mutation: 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.Protein Binding: 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.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)Heterogeneous-Nuclear Ribonucleoproteins: 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.Protein Disulfide-Isomerases: Sulfur-sulfur bond isomerases that catalyze the rearrangement of disulfide bonds within proteins during folding. Specific protein disulfide-isomerase isoenzymes also occur as subunits of PROCOLLAGEN-PROLINE DIOXYGENASE.Mutagenesis, Site-Directed: Genetically engineered MUTAGENESIS at a specific site in the DNA molecule that introduces a base substitution, or an insertion or deletion.Transfection: 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.Pedigree: 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.Restriction Mapping: Use of restriction endonucleases to analyze and generate a physical map of genomes, genes, or other segments of DNA.Oligodeoxyribonucleotides: A group of deoxyribonucleotides (up to 12) in which the phosphate residues of each deoxyribonucleotide act as bridges in forming diester linkages between the deoxyribose moieties.RNA, Fungal: Ribonucleic acid in fungi having regulatory and catalytic roles as well as involvement in protein synthesis.Promoter Regions, Genetic: 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.Escherichia coli: A species of gram-negative, facultatively anaerobic, rod-shaped bacteria (GRAM-NEGATIVE FACULTATIVELY ANAEROBIC RODS) commonly found in the lower part of the intestine of warm-blooded animals. It is usually nonpathogenic, but some strains are known to produce DIARRHEA and pyogenic infections. Pathogenic strains (virotypes) are classified by their specific pathogenic mechanisms such as toxins (ENTEROTOXIGENIC ESCHERICHIA COLI), etc.DNA-Binding Proteins: Proteins which bind to DNA. The family includes proteins which bind to both double- and single-stranded DNA and also includes specific DNA binding proteins in serum which can be used as markers for malignant diseases.Saccharomyces cerevisiae: 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.Globins: A superfamily of proteins containing the globin fold which is composed of 6-8 alpha helices arranged in a characterstic HEME enclosing structure.Kinetics: The rate dynamics in chemical or physical systems.Frameshift Mutation: 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.Mutagenesis: Process of generating a genetic MUTATION. It may occur spontaneously or be induced by MUTAGENS.Protein Structure, Tertiary: The level of protein structure in which combinations of secondary protein structures (alpha helices, beta sheets, loop regions, and motifs) pack together to form folded shapes called domains. Disulfide bridges between cysteines in two different parts of the polypeptide chain along with other interactions between the chains play a role in the formation and stabilization of tertiary structure. Small proteins usually consist of only one domain but larger proteins may contain a number of domains connected by segments of polypeptide chain which lack regular secondary structure.Transcription Factors: Endogenous substances, usually proteins, which are effective in the initiation, stimulation, or termination of the genetic transcription process.Open Reading Frames: 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).Trans-Splicing: 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.Recombinant Proteins: Proteins prepared by recombinant DNA technology.Silencer Elements, Transcriptional: Nucleic acid sequences that are involved in the negative regulation of GENETIC TRANSCRIPTION by chromatin silencing.Thioredoxins: Hydrogen-donating proteins that participates in a variety of biochemical reactions including ribonucleotide reduction and reduction of PEROXIREDOXINS. Thioredoxin is oxidized from a dithiol to a disulfide when acting as a reducing cofactor. The disulfide form is then reduced by NADPH in a reaction catalyzed by THIOREDOXIN REDUCTASE.Repetitive Sequences, Nucleic Acid: Sequences of DNA or RNA that occur in multiple copies. There are several types: INTERSPERSED REPETITIVE SEQUENCES are copies of transposable elements (DNA TRANSPOSABLE ELEMENTS or RETROELEMENTS) dispersed throughout the genome. TERMINAL REPEAT SEQUENCES flank both ends of another sequence, for example, the long terminal repeats (LTRs) on RETROVIRUSES. Variations may be direct repeats, those occurring in the same direction, or inverted repeats, those opposite to each other in direction. TANDEM REPEAT SEQUENCES are copies which lie adjacent to each other, direct or inverted (INVERTED REPEAT SEQUENCES).Sequence Deletion: Deletion of sequences of nucleic acids from the genetic material of an individual.5' Untranslated Regions: 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.Codon, Nonsense: An amino acid-specifying codon that has been converted to a stop codon (CODON, TERMINATOR) by mutation. Its occurance is abnormal causing premature termination of protein translation and results in production of truncated and non-functional proteins. A nonsense mutation is one that converts an amino acid-specific codon to a stop codon.Reverse Transcriptase Polymerase Chain Reaction: 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.Ficusin: A naturally occurring furocoumarin, found in PSORALEA. After photoactivation with UV radiation, it binds DNA via single and double-stranded cross-linking.Regulatory Sequences, Ribonucleic Acid: Sequences within RNA that regulate the processing, stability (RNA STABILITY) or translation (TRANSLATION, GENETIC) of RNA.Models, Molecular: Models used experimentally or theoretically to study molecular shape, electronic properties, or interactions; includes analogous molecules, computer-generated graphics, and mechanical structures.Enhancer Elements, Genetic: Cis-acting DNA sequences which can increase transcription of genes. Enhancers can usually function in either orientation and at various distances from a promoter.DNA Transposable Elements: Discrete segments of DNA which can excise and reintegrate to another site in the genome. Most are inactive, i.e., have not been found to exist outside the integrated state. DNA transposable elements include bacterial IS (insertion sequence) elements, Tn elements, the maize controlling elements Ac and Ds, Drosophila P, gypsy, and pogo elements, the human Tigger elements and the Tc and mariner elements which are found throughout the animal kingdom.Genes: 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.Chickens: Common name for the species Gallus gallus, the domestic fowl, in the family Phasianidae, order GALLIFORMES. It is descended from the red jungle fowl of SOUTHEAST ASIA.Cell Nucleus: 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)Phylogeny: The relationships of groups of organisms as reflected by their genetic makeup.Structure-Activity Relationship: The relationship between the chemical structure of a compound and its biological or pharmacological activity. Compounds are often classed together because they have structural characteristics in common including shape, size, stereochemical arrangement, and distribution of functional groups.Base Composition: The relative amounts of the PURINES and PYRIMIDINES in a nucleic acid.Alleles: Variant forms of the same gene, occupying the same locus on homologous CHROMOSOMES, and governing the variants in production of the same gene product.Ribonuclease H: 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.RNA Processing, Post-Transcriptional: 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.Polypyrimidine Tract-Binding Protein: 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.Phenotype: The outward appearance of the individual. It is the product of interactions between genes, and between the GENOTYPE and the environment.Sequence Analysis, RNA: A multistage process that includes cloning, physical mapping, subcloning, sequencing, and information analysis of an RNA SEQUENCE.DNA, Viral: Deoxyribonucleic acid that makes up the genetic material of viruses.Cross-Linking Reagents: 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.beta-Crystallin A Chain: The acidic subunit of beta-crystallins.Mutation, Missense: 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)Electrophoresis, Polyacrylamide Gel: Electrophoresis in which a polyacrylamide gel is used as the diffusion medium.Genetic Variation: Genotypic differences observed among individuals in a population.Databases, Nucleic Acid: 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.Molecular Weight: The sum of the weight of all the atoms in a molecule.Heterozygote: An individual having different alleles at one or more loci regarding a specific character.Base Pairing: Pairing of purine and pyrimidine bases by HYDROGEN BONDING in double-stranded DNA or RNA.Computational Biology: 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.Protein Conformation: The characteristic 3-dimensional shape of a protein, including the secondary, supersecondary (motifs), tertiary (domains) and quaternary structure of the peptide chain. PROTEIN STRUCTURE, QUATERNARY describes the conformation assumed by multimeric proteins (aggregates of more than one polypeptide chain).Single-Strand Specific DNA and RNA Endonucleases: Enzymes that catalyze the endonucleolytic cleavage of single-stranded regions of DNA or RNA molecules while leaving the double-stranded regions intact. They are particularly useful in the laboratory for producing "blunt-ended" DNA molecules from DNA with single-stranded ends and for sensitive GENETIC TECHNIQUES such as NUCLEASE PROTECTION ASSAYS that involve the detection of single-stranded DNA and RNA.Polymorphism, Single-Stranded Conformational: Variation in a population's DNA sequence that is detected by determining alterations in the conformation of denatured DNA fragments. Denatured DNA fragments are allowed to renature under conditions that prevent the formation of double-stranded DNA and allow secondary structure to form in single stranded fragments. These fragments are then run through polyacrylamide gels to detect variations in the secondary structure that is manifested as an alteration in migration through the gels.Consanguinity: The magnitude of INBREEDING in humans.Expressed Sequence Tags: Partial cDNA (DNA, COMPLEMENTARY) sequences that are unique to the cDNAs from which they were derived.Gene Products, rev: 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.Genes, rev: 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.Virus Replication: 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.RNA, Catalytic: 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.Gene Expression Regulation: 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.Peptide Fragments: Partial proteins formed by partial hydrolysis of complete proteins or generated through PROTEIN ENGINEERING techniques.Viral Proteins: Proteins found in any species of virus.COS Cells: CELL LINES derived from the CV-1 cell line by transformation with a replication origin defective mutant of SV40 VIRUS, which codes for wild type large T antigen (ANTIGENS, POLYOMAVIRUS TRANSFORMING). They are used for transfection and cloning. (The CV-1 cell line was derived from the kidney of an adult male African green monkey (CERCOPITHECUS AETHIOPS).)rev Gene Products, Human Immunodeficiency Virus: Proteins encoded by the REV GENES of the HUMAN IMMUNODEFICIENCY VIRUS.Endopeptidases: A subclass of PEPTIDE HYDROLASES that catalyze the internal cleavage of PEPTIDES or PROTEINS.Poly A: 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.DNA, Bacterial: Deoxyribonucleic acid that makes up the genetic material of bacteria.Tropomyosin: A protein found in the thin filaments of muscle fibers. It inhibits contraction of the muscle unless its position is modified by TROPONIN.Evolution, Molecular: The process of cumulative change at the level of DNA; RNA; and PROTEINS, over successive generations.Phosphorylation: The introduction of a phosphoryl group into a compound through the formation of an ester bond between the compound and a phosphorus moiety.Poly(A)-Binding Proteins: Proteins that bind to the 3' polyadenylated region of MRNA. When complexed with RNA the proteins serve an array of functions such as stabilizing the 3' end of RNA, promoting poly(A) synthesis and stimulating mRNA translation.RNA, Heterogeneous Nuclear: 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.Blotting, Northern: 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.Genes, Recessive: Genes that influence the PHENOTYPE only in the homozygous state.Tetrahymena: A genus of ciliate protozoa commonly used in genetic, cytological, and other research.Chromosome Mapping: Any method used for determining the location of and relative distances between genes on a chromosome.3' Untranslated Regions: The sequence at the 3' end of messenger RNA that does not code for product. This region contains transcription and translation regulating sequences.Gene Expression Regulation, Viral: Any of the processes by which cytoplasmic factors influence the differential control of gene action in viruses.Genome, Human: The complete genetic complement contained in the DNA of a set of CHROMOSOMES in a HUMAN. The length of the human genome is about 3 billion base pairs.Drosophila melanogaster: A species of fruit fly much used in genetics because of the large size of its chromosomes.Trypanosomatina: A suborder of monoflagellate parasitic protozoa that lives in the blood and tissues of man and animals. Representative genera include: Blastocrithidia, Leptomonas, CRITHIDIA, Herpetomonas, LEISHMANIA, Phytomonas, and TRYPANOSOMA. Species of this suborder may exist in two or more morphologic stages formerly named after genera exemplifying these forms - amastigote (LEISHMANIA), choanomastigote (CRITHIDIA), promastigote (Leptomonas), opisthomastigote (Herpetomonas), epimastigote (Blastocrithidia), and trypomastigote (TRYPANOSOMA).Homozygote: An individual in which both alleles at a given locus are identical.Peptides: Members of the class of compounds composed of AMINO ACIDS joined together by peptide bonds between adjacent amino acids into linear, branched or cyclical structures. OLIGOPEPTIDES are composed of approximately 2-12 amino acids. Polypeptides are composed of approximately 13 or more amino acids. PROTEINS are linear polypeptides that are normally synthesized on RIBOSOMES.RNA Helicases: A family of proteins that promote unwinding of RNA during splicing and translation.Adenoviruses, Human: Species of the genus MASTADENOVIRUS, causing a wide range of diseases in humans. Infections are mostly asymptomatic, but can be associated with diseases of the respiratory, ocular, and gastrointestinal systems. Serotypes (named with Arabic numbers) have been grouped into species designated Human adenovirus A-F.Polyadenylation: The addition of a tail of polyadenylic acid (POLY A) to the 3' end of mRNA (RNA, MESSENGER). Polyadenylation involves recognizing the processing site signal, (AAUAAA), and cleaving of the mRNA to create a 3' OH terminal end to which poly A polymerase (POLYNUCLEOTIDE ADENYLYLTRANSFERASE) adds 60-200 adenylate residues. The 3' end processing of some messenger RNAs, such as histone mRNA, is carried out by a different process that does not include the addition of poly A as described here.Bovine papillomavirus 1: A species of DELTAPAPILLOMAVIRUS infecting cattle.Tay-Sachs Disease: An autosomal recessive neurodegenerative disorder characterized by the onset in infancy of an exaggerated startle response, followed by paralysis, dementia, and blindness. It is caused by mutation in the alpha subunit of the HEXOSAMINIDASE A resulting in lipid-laden ganglion cells. It is also known as the B variant (with increased HEXOSAMINIDASE B but absence of hexosaminidase A) and is strongly associated with Ashkenazic Jewish ancestry.Thalassemia: A group of hereditary hemolytic anemias in which there is decreased synthesis of one or more hemoglobin polypeptide chains. There are several genetic types with clinical pictures ranging from barely detectable hematologic abnormality to severe and fatal anemia.Caenorhabditis elegans: A species of nematode that is widely used in biological, biochemical, and genetic studies.Blotting, Southern: A method (first developed by E.M. Southern) for detection of DNA that has been electrophoretically separated and immobilized by blotting on nitrocellulose or other type of paper or nylon membrane followed by hybridization with labeled NUCLEIC ACID PROBES.Afibrinogenemia: A deficiency or absence of FIBRINOGEN in the blood.Gene Deletion: A genetic rearrangement through loss of segments of DNA or RNA, bringing sequences which are normally separated into close proximity. This deletion may be detected using cytogenetic techniques and can also be inferred from the phenotype, indicating a deletion at one specific locus.Drosophila Proteins: Proteins that originate from insect species belonging to the genus DROSOPHILA. The proteins from the most intensely studied species of Drosophila, DROSOPHILA MELANOGASTER, are the subject of much interest in the area of MORPHOGENESIS and development.DEAD-box RNA Helicases: 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.Kidd Blood-Group System: A group of antigens consisting principally of Jk(a) and Jk(b), determined by allelic genes. Amorphs are encountered. Antibodies of these substances are usually weak and quite labile, stimulated by erythrocytes.Polyomavirus: A genus of potentially oncogenic viruses of the family POLYOMAVIRIDAE. These viruses are normally present in their natural hosts as latent infections. The virus is oncogenic in hosts different from the species of origin.beta-Globins: Members of the beta-globin family. In humans, they are encoded in a gene cluster on CHROMOSOME 11. They include epsilon-globin, gamma-globin, delta-globin and beta-globin. There is also a pseudogene of beta (theta-beta) in the gene cluster. Adult HEMOGLOBIN is comprised of two ALPHA-GLOBIN chains and two beta-globin chains.Thiouridine: A photoactivable URIDINE analog that is used as an affinity label.Gene Expression: The phenotypic manifestation of a gene or genes by the processes of GENETIC TRANSCRIPTION and GENETIC TRANSLATION.Syndrome: A characteristic symptom complex.Guanosine: A purine nucleoside that has guanine linked by its N9 nitrogen to the C1 carbon of ribose. It is a component of ribonucleic acid and its nucleotides play important roles in metabolism. (From Dorland, 28th ed)
... is found in an intronic sequence close to the exon. The intronic sequence includes a 5' splice site. The predicted double ... The intronic sequence involved contains a 5' donor splice site. Editing also occurs in rat. Editing of GluR-3 is regulated in ... Despite similar sequences to the Q/R site of GluR-B, editing a this site does not occur in GluR-3 pre-mRNA. Editing results in ... The absence of the Q/R site editing in this glutamate receptor subunit is due to the absence of necessary intronic sequence ...
These mutations include nonsense, missense, splice site mutation, and intragenic deletions/insertions. Deletion/duplication ... such as sequence analysis, deletion/duplication analysis, and cytogenetics/ FISH analysis. Sequence analysis of exon 1 (TWIST1 ... analysis identifies mutations in the TWIST1 gene that are not readily detected by sequence analysis. Common methods include PCR ...
... around the splice sites, and an extended hairpin (H1) that brings the splice sites together (see figure). The sequence of the ... Stem-loop structures around the splice sites and IRE1-specific sequence motifs are both necessary and sufficient for splicing ... Recognition of the intron splice sites is mediated by a base-paired secondary structure of the mRNA that forms at the exon/ ... Sidrauski C, Walter P (1997). "The transmembrane kinase Ire1p is a site-specific endonuclease that initiates mRNA splicing in ...
These web-based BLAT servers keep the index in memory for users to input their query sequences. Once the query sequence is ... splice sites). BLAT is less sensitive than BLAST. BLAT can be used either as a web-based server-client program or as a stand- ... provide step by step protocols for how to use BLAT to: Map an mRNA/cDNA sequence to a genomic sequence; Map a protein sequence ... BLAT can handle long database sequences, however, it is more effective with short query sequences than long query sequences. ...
... splice site and branch site sequences. Minor spliceosome consists of U11, U12, U4atac, and U6atac, together with U5 and an ... The results suggested a new type of introns with ATATCCTT 5' splice site and YCCAC 3' splice site and an almost invariant ... A search for small nuclear RNA sequences that are complementary to these splice sites, suggested U12 snRNA (matches 3' sequence ... Hall SL, Padgett RA (1994). "Conserved sequences in a class of rare eukaryotic nuclear introns with non-consensus splice sites ...
Senapathy, P.; Shapiro, M. B.; Harris, N. L. (1 January 1990). "Splice junctions, branch point sites, and exons: sequence ... "Splice-Site Analyzer Tool". ibis.tau.ac.il. Southampton, University of. "DBASS3 - Aberrant Splice Site Database". www.dbass.org ... S&S has been implemented for finding splice sites and mutations in several tools such as Human Splice Finder, SROOGLE, Splice- ... Mueller, Nancy; van Bel, Nikki; Berkhout, Ben; Das, Atze T. (1 November 2014). "HIV-1 splicing at the major splice donor site ...
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 ... Straub T, Grue P, Uhse A, Lisby M, Knudsen BR, Tange TO, Westergaard O, Boege F (October 1998). "The RNA-splicing factor PSF/ ... Proteins in the DHBS family include mammalian SFPQ (splicing factor, proline- and glutamine-rich; a.k.a. PSF), NONO (Non-POU ...
... separated by non-coding sequences (introns). (Splice sites are themselves another signal that eukaryotic gene finders are often ... The first is a smaller classifier, identifying donor splice sites and acceptor splice sites as well as start and stop codons. ... July 2009). "mGene.web: a web service for accurate computational gene finding". Nucleic Acids Res. 37 (Web Server issue): W312- ... each position is a score based on whether the network thinks the window contains a donor splice site or an acceptor splice site ...
Coding sequences and splice sites of LPIN2 were sequenced in the patient and her mother. A homozygous single-basepair change ... Al-Mosawi, Al-Saad; Ijadi-Maghsoodi, El-Shanti (2007). "A splice site mutation confirms the role of LPIN2 in Majeed syndrome". ... was detected in the donor splice site of exon 17 (c.2327+1G>C) in the patient; her mother was heterozygous at this site. These ... Chronic recurrent multifocal osteomyelitis (CRMO) ("multifocal" because it can erupt in different sites, primarily bones; " ...
D. A. Nielsen, G. L. Jenkins, K. M. Stefanisko, K. K. Jefferson & D. Goldman (April 1997). "Sequence, splice site and ...
It starts translation at a different start codon than variant 1 by utilizing an alternate splice site. The 5' region is ... The primary sequence for FAM227A is isoform 1 with accession number: NP_001013669.1. It is 570 amino acids long. There are 9 ... "FAM227A family with sequence similarity 227 member A [Homo sapiens (human)] - Gene - NCBI". www.ncbi.nlm.nih.gov. Retrieved ... FAM227A is present in species of mammals, birds and reptiles, and gene alignment sequences have shown that FAM227A is a rapidly ...
"Exome Sequencing Identifies a recessive PIGN splice site mutation as a cause of Syndromic Congenital Diaphragmatic Hernia". ... Two alternatively spliced variants, which encode an identical isoform, have been reported. [provided by RefSeq, Jul 2008]. ...
The protein complex binds to the branchpoint sequence (BPS) in the pre-mRNA, aiding in splice site recognition. The role of the ... "BBP Involved in Splice Site Recognition". Archived from the original on 2010-05-31. Rymond, B. C. (2010). "The branchpoint ... "The Splicing Factor BBP Interacts Specifically with the Pre-mRNA Branchpoint Sequence UACUAAC". ...
As a graduate student, Gish applied the Quine-McCluskey algorithm to the analysis of splice site recognition sequences. In 1985 ... by a novel approach that combined information from donor and acceptor splice site models with information from sequence ... in part to aid multiplexing with MPBLAST and in part to aid analysis of segmented query sequences from shotgun sequencing ... Construction of the DFA was O(n), where n is the sum of the lengths of the query sequences. The DFA could then be used to scan ...
The splice donor and acceptor sites present within the gene all conform to GT/AC rule of splicing. The DNA sequence in the ... sequences resembling the Sp1 transcription factor binding site, and two cAMP receptor binding sites upstream of the cap. The ... There is a "TATA box"-like sequence and a "CAAT present upstream from the cap site. There are also several sets of repeats, ... The E1-alpha subunit contains the E1 active site and plays a key role in the function of the PDH complex. The PDHA1 gene has ...
Splicing by overhang extension (SOE) PCR. It is used to insert specific mutations at specific points in a sequence or to splice ... This method has an advantage over other gene splicing techniques in not requiring restriction sites. To get higher yields, some ... As in most PCR reactions, two primers-one for each end-are used per sequence. To splice two DNA molecules, special primers are ... The primer may contain a single substitution or contain a new sequence at its 5' end. If a deletion is required, a sequence ...
... which forms a bulge at the branch point binding sequence. In addition, U6 snRNA associates with U2 snRNA and the 5′ splice site ... However, in yeast, introns do not contain a polypyrimidine tract at their 3′ splice site. In order for splicing to occur ... splice site by U1 snRNA, U1 snRNA binds to this point. As soon as this bond forms, U2 snRNA binds to the branch point site, ... splice site, thus starting the first of two transesterification reactions that mediate splicing. After recognition of the pre- ...
Parkinson DB, Thakker RV (May 1992). "A donor splice site mutation in the parathyroid hormone gene is associated with autosomal ... Niall HD, Sauer RT, Jacobs JW, Keutmann HT, Segre GV, O'Riordan JL, Aurbach GD, Potts JT (Feb 1974). "The amino-acid sequence ... Andreatta RH, Hartmann A, Jöhl A, Kamber B, Maier R, Riniker B, Rittel W, Sieber P (1973). "[Synthesis of sequence 1-34 of ... Vasicek TJ, McDevitt BE, Freeman MW, Fennick BJ, Hendy GN, Potts JT, Rich A, Kronenberg HM (Apr 1983). "Nucleotide sequence of ...
"Whole exome sequencing identifies a novel splice-site mutation in ADAMTS17 in an Indian family with Weill-Marchesani syndrome ... The protein encoded by this gene has a high sequence similarity to the protein encoded by ADAMTS19, another family member. The ...
2004). "A novel PRPF31 splice-site mutation in a Chinese family with autosomal dominant retinitis pigmentosa". Mol. Vis. 10: ... 2004). "Complete sequencing and characterization of 21,243 full-length human cDNAs". Nat. Genet. 36 (1): 40-5. doi:10.1038/ ... A mutation in PRPF31 is one of 4 known mutations in splicing factors which are known to cause retinitis pigmentosa. The first ... PRPF31 is the gene coding for the splicing factor hPRP31. It is essential for the formation of the spliceosome hPRP31 is ...
Bowtie (sequence analysis) Trapnell, C.; Pachter, L.; Salzberg, S. L. (16 March 2009). "TopHat: discovering splice junctions ... using Bowtie first and then mapping to a reference genome to discover RNA splice sites de novo. TopHat was originally developed ... TopHat is a bioinformatic sequence analysis package tool for fast and high throughput alignment of shotgun cDNA sequencing ...
... site. The 5' splice site region possesses sequence complementarity with the 5' splice site of the eukaryotic U12 type pre-mRNA ... splice site (functionally equivalent to U2 snRNA). U11 snRNA has a stem-loop structure with a 5' end as splice site sequence (5 ... Both the 5' splice site and the Sm binding site are highly conserved in all species. Also, stem loop III is either a possible ... splice site and branchpoint sequence of the mRNA respectively, through base pairing. U11 snRNP binds to a tandem repeat known ...
These mutations included multiple Nonsense mutations and splice site mutations throughout the gene. missense mutations were ... domain and Nuclear localization sequences were required for BAP1 to suppress cell growth. In 2010, Exome sequencing identified ... Sequencing efforts demonstrated worse outcomes in patients with BAP1 mutated clear cell renal cell carcinoma. . Two studies ... Zhou ZR, Zhang YH, Liu S, Song AX, Hu HY (Jan 2012). "Length of the active-site crossover loop defines the substrate ...
It has an alternative splice site in the 5' region that causes the translation to initiate downstream at an in frame AUG. ... A nuclear localization sequence of 5 positive amino acids is found near the 5' end indicating its transport to the nucleus. The ... This transcript variant has an alternate splice site in the central coding region that does not alter the reading frame. ... Variant 1 is the longest and variant 2 and 3 are spliced into shorter mRNA strands. There is also a predicted variants X1-X7. ...
"Spliceman-a computational web server that predicts sequence variations in pre-mRNA splicing" (PDF). Bioinformatics. 28 (7): ... Each hexamer of DNA base pairs has a positional distribution near splice sites where it is most likely to occur. Point ... "Transcription-coupled RNA surveillance in human genetic diseases caused by splice site mutations". Human Molecular Genetics. 24 ... The Spliceman tool is available for free online on the website for the Fairbrother Lab. A second version of the tool, Spliceman ...
Large-scale sequencing of the chimpanzee genome is now imminent.. ". Olson M, Varki A. Sequencing the chimpanzee genome: ... alternative splicing；將穿插在內含子中的外顯子以選擇性的方式進行轉錄），這使得一個基因能夠製造出多種不同的蛋白質，且人類的蛋白質組規模也較前述的兩個物種更
Due to this algorithm, ProSplign is accurate in determining splice sites and tolerant to sequencing errors. ... Sequence Read Archive (SRA) The Sequence Read Archive (SRA) stores sequencing data from the next generation of sequencing ... FTP: Sequence Read Archive (SRA) Download Facility This site contains next-generation sequencing data organized by the ... Due to this algorithm, Splign is accurate in determining splice sites and tolerant to sequencing errors. ...
Citations may include links to full-text content from PubMed Central and publisher web sites. ... U5 snRNA interacts with exon sequences at 5 and 3 splice sites.. Newman AJ1, Norman C. ... splice sites. This pattern of interactions is strikingly reminiscent of exon recognition events in group II self-splicing ... splice sites and facilitate processing of dead-end lariat intermediates to mRNA. Activation of aberrant 5 cleavage sites ...
... splice sites of human beta-globin IVS 1 revealed that exon sequences play an important role in the relative use of the ... duplicated sites. These studies also show that the proximity of the 5 an … ... Analysis of the in vitro splicing products of RNA precursors containing tandem duplications of the 5 or 3 ... A role for exon sequences and splice-site proximity in splice-site selection Cell. 1986 Aug 29;46(5):681-90. doi: 10.1016/0092- ...
Joint Prediction of Branchpoint and Splice Acceptor Sites in pre-mRNA Transcripts Using Sequence to Sequence Networks ... sequence during each stage of spliceosome sequences, splice sites, and the branchpoint Identification of proteins that interact ... sequence during each stage of spliceosome sequences, splice sites, and the branchpoint Identification of proteins that interact ... Splice Sites, and the Branchpoint Sequence during Each by Mol Cell Biol, R Reed, M D Chiara, O Gozani, M Bennett, P Champion- ...
... splice site sequence of the human beta-globin intervening sequence 1, which includes the sequence UUAGG. Proteins in this ... Nuclear proteins that bind the pre-mRNA 3 splice site sequence r(UUAG/G) and the human telomeric DNA sequence d(TTAGGG)n.. F ... Nuclear proteins that bind the pre-mRNA 3 splice site sequence r(UUAG/G) and the human telomeric DNA sequence d(TTAGGG)n. ... Nuclear proteins that bind the pre-mRNA 3 splice site sequence r(UUAG/G) and the human telomeric DNA sequence d(TTAGGG)n. ...
We constructed SP6-human beta-globin derivative plasmids that included possible donor site (5 splice site) sequences at a ... The active donor site sequences included a 9-nucleotide consensus sequence, 14- or 16-nucleotide sequences at the human beta- ... Short donor site sequences inserted within the intron of beta-globin pre-mRNA serve for splicing in vitro.. A Mayeda, Y Ohshima ... Short donor site sequences inserted within the intron of beta-globin pre-mRNA serve for splicing in vitro. ...
... splice site and 5 splice site, respectively. Here, two or more splice sites are recognized at one end of the exon. The fourth ... They must have conserved splice site patterns (e.g. a GT 5 intron splice site cannot be combined with a AC 3 splice site) and ... Predicting mutually exclusive spliced exons based on exon length, splice site and reading frame conservation, and exon sequence ... terminal exons that are spliced in a mutually exclusive manner and share sequence similarity, similar length, and splice site ...
Sequencing of the amplified cDNA revealed the absence of the entire exon 14. Other COL6A1 mutations affecting the same splice ... C in the COL6A1 gene on the splicing at the donor site was evaluated by NetGene2 , Humans Splicing Finder , Splice Site ... A heterozygous splice site mutation in COL6A1 leading to an in-frame deletion of the alpha1(VI) collagen chain in an italian ... A novel de novo COL6A1 mutation emphasizes the role of intron 14 donor splice site defects as a cause of moderate-progressive ...
... these mutations are assumed to interfere with splicing by falsely matching the AG consensus sequence of a 3′ splice site ... splice sites (reviewed in ref. 8). Despite etiologic progress, the relationships between disease-causing pre-mRNA splice site ... of these mutations affect regulatory splice site signals (3, 4). One of the earliest reports of a splice site mutation as a ... and UAP56 splicing proteins to the pre-mRNA site. Alternatively, so-called "splice-site switching" oligonucleotides (SSOs) are ...
Splice Site Score Calculation. The score expresses how similar the splice sites fits the consensus sequence. A 100% match to ... Input sequence (either the 5splice site or the 3 splice site):. Note that:. *it is case insensitive *characters other than ... A perfect 5 splice site AAG,gtaag t would have a score of 12.6. The mean score of the 3 splice site in constitutive exons is ... For a 5 splice site, you must specify 3 nt in exon and 6 nt in intron. Exon. Intron. A/C A G. g t a a g t consensus entry For ...
... splice sites (A5SS, 167), and alternative 3 splice sites (A3SS, 302) is 7.3, 7.4, 5.1, and 5.9-fold higher, respectively, than ... Alternatively spliced introns had longer lengths, higher GC contents, and lower splice site scores than constitutive introns. ... Further analysis demonstrated that the isoform relative frequencies were correlated with the splice site scores of the isoforms ... Analyses of alternative splicing events revealed that the number of all alternative splicing events (10034), intron retentions ...
Although nonsense mutations have been associated with the skipping of specific constitutively spliced exons in selected genes, ... Molecular Sequence Data * Open Reading Frames* * Ornithine-Oxo-Acid Transaminase / genetics * Polymerase Chain Reaction ... Maintenance of an open reading frame as an additional level of scrutiny during splice site selection Nat Genet. 1994 Oct;8(2): ... premature termination codons are identified as determinants of splice site selection. Nonsense codon recognition prior to RNA ...
Citations may include links to full-text content from PubMed Central and publisher web sites. ... Boxes list the number of genes with 1+ nonsynonymous cSNP, splice-site SNP, or coding indel ("NS/SS/I") meeting specified ... Targeted capture and massively parallel sequencing of 12 human exomes.. Ng SB1, Turner EH, Robertson PD, Flygare SD, Bigham AW ... Although DNA sequencing costs have fallen markedly, they remain far from what is necessary for rare and novel variants to be ...
Comparative analysis of sequence features involved in the recognition of tandem splice sites Authors: Ralf Bortfeldt, Stefanie ... Alternative splicing at NAGNAG acceptors in Arabidopsis thaliana SR and SR-related protein-coding genes Authors: Stefanie ... De novo 454 sequencing of barcoded BAC pools for comprehensive gene survey and genome analysis in the complex genome of barley ... By using this website, you agree to our Terms and Conditions, Privacy statement and Cookies policy. ...
Splice site prediction in Arabidopsis thaliana pre-mRNA by combining local and global sequence information. . Biblioteca ... coding context and distances between potential splice sites. In this approach, the prediction of splice sites mutually affect ... Splice site prediction in Arabidopsis thaliana pre-mRNA by combining local and global sequence information - Descarga este ... The combined approach drastically reduces the large amount of false positive splice sites normally haunting splice site ...
SA, splice acceptor site; SD, splice donor site; LTR, long terminal repeat sequence; pA, polyadenylation signal; puro, ... thought you would like to see the PNAS web site. ... The Foxo4 targeting vector contained 6.5 kb of genomic sequence ... cassette and 1.5 kb of genomic sequence of intron 1. The Foxo4 targeting vector also had a polyoma enhancer/herpes simplex ... such as lack of some phosphorylation sites conserved in other members and predominant nuclear localization under serum or ...
SROOGLE is a web server that makes splicing signal sequence and scoring data available to the biologist in an integrated, ... browser output displays the four core splicing signals with scores based on nine different algorithms and highlights sequences ... PubMed Link: SROOGLE: webserver for integrative, user-friendly visualization of splicing signals. ... The input consists of the sequence of an exon and flanking introns. ...
Although splice site sequences adjacent to the affected exons showed no significant difference compared to the total exons, ... Although splice site sequences adjacent to the affected exons showed no significant difference compared to the total exons, ... RNA sequence analyses revealed that both wild type and mutants affected splicing of approximately 3,000 genes. ... In vitro splicing reaction also revealed that mutant proteins could support splicing reaction and associate with pre-mRNA and ...
... based on the characteristics of base composition of sequences and conservative of nucleotides at exon/intron splicing site, a ... The predicted successful rates are higher than 80%. These results can be used in sequence annotation. ... intron and intergenic sequence are predicted. The results show that overall predicted accuracies are 91.1% and 88.4%, ... initia-tion and termination site of translation, 12 position parameters are selected as diversity source. And three kinds of ...
The IVS6-1 (c403-1G>C) mutation resulted from a cryptic splice site in MYL2 causing a frameshift and replacement of the last 32 ... The IVS6-1 (c403-1G,C) mutation resulted from a cryptic splice site in MYL2 causing a frameshift and replacement of the last 32 ... Figure 1. (A) Amino acid sequences of myosin RLC WT and IVS6-1 mutant protein. IVS6-1 is a splice site mutation 1 (c403-1G,C) ... The IVS6-1 (c403-1G,C) mutation resulted from a cryptic splice site in MYL2 causing a frameshift and replacement of the last 32 ...
Citations may include links to full-text content from PubMed Central and publisher web sites. ... Mutation screening of EXT1 and EXT2 by direct sequence analysis and MLPA in patients with multiple osteochondromas: splice site ... The number of the splice site mutations detected was larger than expected from the literature. In addition, with the MLPA four ... In patients suspected to be affected by MO, we recommend a quantitative analysis such as MLPA, followed by direct sequence ...
... intervening sequence; KSRP, KH type splicing regulatory protein; RRE, Rev response element; RT-PCR, reverse-transcription PCR. ... that RNA splice sites suppress editing of precursor RNAs when placed proximal or distal to the editing site. Processed RNAs ... Commitment of apolipoprotein B RNA to the splicing pathway regulates cytidine-to-uridine editing-site utilization. Mark P. ... Mutation of both the splice donor and acceptor sites was necessary for RNAs to be edited efficiently. The results suggested ...
Minimal Conditions for Exonization of Intronic Sequences; 5′ Splice Site Formation in Alu Exons. Sorek, R., Lev-Maor, G., ... The Birth of an Alternatively Spliced Exon: 3′ Splice-Site Selection in Alu Exons. Lev-Maor, G., Sorek, R., Shomron, N., and ... Intronic Sequences Flanking Alternatively Spliced Exons Are Conserved Between Human and Mouse. Sorek, R. and Ast, G.. Jul 01, ... Bridging Expressed Sequence Alignments Through Targeted cDNA Sequencing. Xie, H., Diber, A., Pollock, S., Nemzer, S., Safer, H ...
Apollo is a web-based, collaborative genomic annotation editing platform. We need annotation editing tools to modify and refine ... sequence) v Splicing "signals" (from the point of view of an intron): • There is a 5 end splice "signal" (site): usually GT ( ... 52 SPLICE SITES Becoming Acquainted with Web Apollo. SIMPLE CASES Zoom to review non--‐canonical splice site warnings. Although ... splice sites 51 ORFs AND SPLICE SITES Becoming Acquainted with Web Apollo. SIMPLE CASES ...
The sequence BAC86747 differs from that shown. Unlikely isoform. Aberrant splice sites.Curated ... Sequence databases. Select the link destinations:. EMBL nucleotide sequence database. More...EMBLi. GenBank nucleotide sequence ... help/sequence_caution target=_top>More...,/a>,/p>Sequence cautioni. The sequence AAH34353 differs from that shown. Reason: ... The sequence of this isoform differs from the canonical sequence as follows:. 205-251: Missing.. 439-439: E → EQKYWEALNSEQ. ...
GeneCDNAProteinGeneticMolecularAnnotationExonsIntronsIntronicPredictionJunctionsGenomesAberrantMassively parallelCryptic splice siteRecognitionAnnotationConstitutiveDownstreamNucleotidePrecursorGenomic sequenceOccurExomeAlternatively spliced formsEukaryotesTranscriptomePromoterGeneticsArabidopsisGene expressionSignalsAcceptor siteCassette exonDonor and acceptor sitesDinucleotidesDifferentialBranchProtein coding seDrosophilaBioinformaticsOrganism
- For example, a population set provides information on genetic variation within an organism, while a phylogenetic set may contain sequences, and their alignment, of a single gene obtained from several related organisms. (unt.edu)
- A collection of human gene-specific reference genomic sequences. (unt.edu)
- Several types of different alternative splice forms exist including exon skipping, differential splicing of exons at their 3'- or 5'-end, intron retention, and mutually exclusive splicing. (biomedcentral.com)
- The latter term is used for clusters of internal exons that are spliced in a mutually exclusive manner. (biomedcentral.com)
- This precondition provides restrictions to the search for candidate exons concerning their length, splice site conservation and reading frame preservation, and overall homology. (biomedcentral.com)
- Thus, WebScipio should be able to identify mutually exclusive spliced exons in any query sequence from any species with a very high probability. (biomedcentral.com)
- It is important to note that the term mutually exclusive splicing is only used for these specific clusters of exons. (biomedcentral.com)
- Mutually exclusive splicing demands a specific mechanism for the regulated splicing of exactly one of the exons of such a cluster. (biomedcentral.com)
- Although splice site sequences adjacent to the affected exons showed no significant difference compared to the total exons, exonic motif analyses with both inclusion- and exclusion-enhanced exons demonstrated that wild-type and mutants have different binding sequences in exons. (frontiersin.org)
- In this paper, based on the characteristics of base composition of sequences and conservative of nucleotides at exon/intron splicing site, a least increment of diversity al-gorithm (LIDA) is developed for studying and predicting three kinds of coding exons, introns and intergenic regions. (scirp.org)
- Paradoxically, clonal expansion may also be enhanced by HIV expression that leads to splicing between HIV donor splice sites and downstream human exons. (nature.com)
- During splicing, introns are removed and exons are joined together. (wikipedia.org)
- The information necessary for the cell to join all the useful parts, or protein coding exons, together correctly is located within the sequence of that gene. (healthcanal.com)
- Mutations that affect this splicing information are often very disruptive to gene function, causing entire exons (the scenes in a movie) to be lost from the final product. (healthcanal.com)
- Despite this, a patient carrying a mutation that results in a faulty splicing, Fairbrother said, may eventually have a brighter outlook than a patient who has mutations in the exons themselves. (healthcanal.com)
- For example, a naturally occurring splice variant containing three additional exons deactivated 20-fold more slowly when combined with β. (jneurosci.org)
- In eukaryotes, trans-splicing is a special event in RNA processing where exons from two different primary RNA transcripts are joined from end to end and then ligated. (biomedcentral.com)
- As intron 1 separates noncoding and coding exons, differential utilization of its 3′ splice site by the uridine- and adenosine-containing pre-mRNAs would be predicted to result in distinct representation of mature transcripts with short and long 5′ untranslated regions (UTRs) with potential effects on translation. (diabetesjournals.org)
- Alternative splicing, also referred to as differential splicing, is a process where the RNA exons of the RNA that is produced by transcription of a gene are reconnected in several different ways during RNA splicing. (brighthub.com)
- In mRNAs after splicing, one of two exons is retained, but not both. (brighthub.com)
- Exons 3 and 5 possess alternative splice sites. (diabetesjournals.org)
- Sequence variations within splice sites may pose problems in the interpretation of their pathogenic effect, especially when these variations occur outside the highly conserved /gt (donor or 5′ site) and ag/ (acceptor or 3′ site) consensus dinucleotides that immediately flank most exons. (bmj.com)
- note the obligatory physiological alternative splice between either the IIIb or IIIc exons. (bmj.com)
- A comprehensive analysis of The Cancer Genome Atlas (TCGA) project RNA sequencing (RNA-seq) data from 16 tumor types and matched normal tissue revealed evidence of global alternative splicing involving a variety of splicing junctions, including cassette exons, retrained introns, and competing 5′ and 3′ splice sites (SSs). (bloodjournal.org)
- Other splicing outcomes include alternative 5′ or 3′ splice sites (mutually exclusive exons, coordinate cassette exons, and alternative first and last exons are not shown). (bloodjournal.org)
- The yellow color in exons 1 and 2 represents exonic sequence that is excluded when splicing into an alternative cryptic splice site occurs, as indicated by the dashed lines at the bottom of each cartoon. (bloodjournal.org)
- Hollywood exon annotation database - A website for querying a relational database of constitutive and alternative human exons, by using biological and descriptive features. (github.com)
- We generated ~1.6 Gb of sequence data, with >87% coverage of exons with a high quality genotype. (genome.gov)
- The first stage in RNA splicing is recognition by the spliceosome of splice sites between introns and exons. (evolutionnews.org)
- This is followed by the second transesterification reaction which results in the splicing together of the two flanking exons. (evolutionnews.org)
- The set includes non-synonymous changes, splice site variants, variants in UTRs, and SNPs flanking exons. (sanger.ac.uk)
- Exons were sequenced in the standard DNA panel (as described above) and patient samples as appropriate, to identify additional SNPs for association studies or direct detection of mutations. (sanger.ac.uk)
- However, changes in the splice sites in introns can lead to deletion of exons or inclusion of introns present next to them. (news-medical.net)
- Many cancers are associated with mutations in intronic splice sites which lead to deletion of essential exons. (news-medical.net)
- This pattern of interactions is strikingly reminiscent of exon recognition events in group II self-splicing introns and is consistent with the notion that U5 snRNA may be related to a specific functional domain from a group II-like self-splicing ancestral intron. (nih.gov)
- The first type is exon skipping, in which an exon, also called cassette exon, is spliced out of the transcript together with its flanking introns. (biomedcentral.com)
- Alternatively spliced introns had longer lengths, higher GC contents, and lower splice site scores than constitutive introns. (biomedcentral.com)
- The input consists of the sequence of an exon and flanking introns. (pitt.edu)
- For many eukaryotic introns, splicing is carried out in a series of reactions which are catalyzed by the spliceosome , a complex of small nuclear ribonucleo proteins ( snRNPs ). (wikipedia.org)
- Self-splicing introns , or ribozymes capable of catalyzing their own excision from their parent RNA molecule, also exist. (wikipedia.org)
- As part of the RNA processing pathway, introns are removed by RNA splicing either shortly after or concurrent with transcription . (wikipedia.org)
- Within introns, a donor site (5' end of the intron), a branch site (near the 3' end of the intron) and an acceptor site (3' end of the intron) are required for splicing. (wikipedia.org)
- The major spliceosome splices introns containing GU at the 5' splice site and AG at the 3' splice site. (wikipedia.org)
- Although this spliceosome shares many properties with the more abundant U2-dependent (U2) intron spliceosome, four of the five small nuclear RNAs (snRNAs) required for splicing are different and specific for the unique splicing of U12 introns. (springer.com)
- Evidence in plants so far indicates that splicing signals of plant U12 introns and their splicing machinery are similar to U12 intron splicing in other eukaryotes. (springer.com)
- In addition to the high conservation of splicing signals, plant U12 introns also retain unique characteristic features of plant U2 introns, such as UA-richness, which suggests a requirement for plant-specific components for both the U2 and U12 splicing reaction. (springer.com)
- This chapter compares U12 and U2 splicing and reviews what is known about plant U12 introns and their possible role in gene expression. (springer.com)
- Chang W-C, Chen Y-C, Lee K-C, Tarn W-Y (2007) Alternative splicing and bioinformatics analysis of human U12-type introns. (springer.com)
- Dietrich RC, Incorvaia R, Padgett RA (1997) Terminal intron dinucleotide sequences do not distinguish between U2- and U12-dependent introns. (springer.com)
- Dietrich RC, Shukla GC, Fuller JD, Padgett RA (2001b) Alternative splicing of U12-dependent introns in vivo responds to purine-rich enhancers. (springer.com)
- Frilander MJ, Steitz JA (1999) Initial recognition of U12-dependent introns requires both U11/5′ splice-site and U12/branchpoint interactions. (springer.com)
- This differs from the exon skipping mode due to the sequence that is retained not being flanked by introns. (brighthub.com)
- The second class of exception to splice site consensus is U12 introns, a minor class of rare introns with splice site sequences that are very different from the standard consensus, but which are very similar to each other (reviewed by Burge et al 1999 and Tarn and Steitz 1997 . (umd.edu)
- Retained intron (RI): A sequence may be spliced out as an intron or retained, and there are no flanking introns. (github.com)
- For example, one could ask, how much of our introns could be completely deleted without adversely affecting alternative splicing? (blogspot.com)
- Fifteen introns, ranging from 36 to 71 bp, interrupted the coding sequence. (sciencemag.org)
- Introns are also non-coding regions, and often mutations and alterations in introns and intronic splice sites do not receive much attention. (news-medical.net)
- Introns may also contain regulatory elements, and mutations may lead to destruction of those sequences leading to change in the gene expression. (news-medical.net)
- i.e. introns can insert themselves into the homologous site in an intron-less allele (intron homing), or less frequently, they may spread into a new site in the same or a different gene. (biomedsearch.com)
- Group I introns may also insert into the natural intron insertion site at the RNA level, and subsequently become stably integrated into the host genome. (biomedsearch.com)
- Thick black lines represent cDNA sequence, and thin lines represent intronic sequence (with diagonal slash marks if not drawn to scale). (nih.gov)
- However, it is noted that the specific sequence of intronic splicing elements and the number of nucleotides between the branchpoint and the nearest 3' acceptor site affect splice site selection. (wikipedia.org)
- The editing complimentary sequence (ECS) is found in an intronic sequence close to the exon. (wikipedia.org)
- The intronic sequence includes a 5' splice site. (wikipedia.org)
- The intronic sequence involved contains a 5' donor splice site. (wikipedia.org)
- The absence of the Q/R site editing in this glutamate receptor subunit is due to the absence of necessary intronic sequence required to form a duplex. (wikipedia.org)
- 4 ⇓ - 6 The spliceosome is a multiprotein complex consisting of 5 small nuclear ribonucleoproteins (snRNPs) and more than 150 proteins that recognizes the elements near intron-exon boundaries and the branch site that catalyzes the excision of intronic regions. (bloodjournal.org)
- Additional trans -acting factors including SR proteins bind the cis -regulatory sequences (exonic and intronic silencers and enhancers) to promote or prevent spliceosome assembly. (bloodjournal.org)
- Splicing signals can be divided into those at the splice stes per se and auxiliary or contextual signals, such as exonic splicing enhancers ( ESEs ), intronic splicing enhancers, exonic splicing silencers (ESSs) and intronic splicing enhancers. (umd.edu)
- These cis-acting elements generally include the splicing enhancers related to exon-inclusion enhancement, splicing silencers related to exon-inclusion inhibition, the intronic branch point and the polypyrimidine tract ( 12 , 13 ). (spandidos-publications.com)
- Sequence motif finding, Splice site prediction, Computational gene findin. (hopkinsmedicine.org)
- In addition to splice site prediction, the web site allows you to browse the features that contribute to the strength (or weakness) of any given site. (umd.edu)
- Right now, feature browsing is only available for mammalian sites (using a classifier trained on human data), but you can carry out splice site prediction on Arabidopsis as well. (umd.edu)
- Accurate Splice Site Prediction Using Support Vector Machines. (biomedcentral.com)
- ASPicDB - Alternative Splicing PredICtion DataBase. (github.com)
- A modification to an "ace" gene prediction program by computer scientists at Washington University in St. Louis now enables scientists to predict the very beginnings of gene transcription start sites and where the first splice occurs thereby defining the first exon of the gene. (bio-medicine.org)
- All present gene finding systems ?except for N-SCAN ?either ignore the UTR splice sites or incorrectly incorporate them into some protein-coding segment, making gene prediction a none-too-sure industry. (bio-medicine.org)
- As more genomes are sequenced, there is an increasing need for automated gene prediction. (demokritos.gr)
- One of the subproblems of the gene prediction, is the splice sites recognition. (demokritos.gr)
- In applications of bioinformatics and text processing, such as splice site recognition and spam detection, large amounts of training sequences are available and needed to achieve sufficiently high prediction performance on classification or regression tasks. (videolectures.net)
- Accurate Splice Site Prediction for Caenorhabditis Elegans, pages 277-298. (videolectures.net)
- Please be patient--splice site prediction may take a while. (fruitfly.org)
- A total of 14305 splice junctions were discovered. (biomedcentral.com)
- Be warned however, splicing junctions are HIGHLY degenerate especially in humans. (bio.net)
- G-Mo.R-Se - maps splice junctions to genome. (github.com)
- HMMSplicer - discovery canonical and non-canonical splice junctions in short read datasets. (github.com)
- JunctionSeq - identify differential splice junctions. (github.com)
- SpliceMap - discover and align splice junctions for RNA-Seq reads. (github.com)
- TopHat - map splice junctions for RNA-Seq reads. (github.com)
- The exon junction complex (EJC) is a protein complex comprised of several protein components (RNPS1, Y14, SRm160, Aly/REF and Magoh) left behind near splice junctions by the splicing process ( Hir and Andersen, 2008 ). (evolutionnews.org)
- The genomes of Tr , Ta , and Tv have been sequenced, providing invaluable resources for the study of Trichoderma metabolism. (biomedcentral.com)
- i.e. of a set of proteins thought to be expressed by organisms whose genomes have been completely sequenced. (uniprot.org)
- The size and complexity of their genomes (∼20-40 Gb, 2 n = 24) have delayed the arrival of a well-annotated reference sequence. (genetics.org)
- The gene models for loblolly pine have the highest median and mean intron lengths of 24 fully sequenced plant genomes. (genetics.org)
- Pruitt KD, Tatusova T, Maglott DR. NCBI Reference Sequence (RefSeq): a curated non-redundant sequence database of genomes, transcripts and proteins . (ucsc.edu)
- There are now complete genome sequences available for 12 Drosophila species , but the annotations for those genomes aren't easily accessible for most people. (scienceblogs.com)
- In under 10 years, massively parallel next generation sequencing has led to the routine sequencing of exomes and whole genomes. (mdpi.com)
- The sequencing of the human and other genomes has ushered in the age of functional genomics. (google.com)
- N-SCAN has proven to be the best program available at finding both the transcription start site (TSS) and the complete first exon in both the human and fruit fly genomes. (bio-medicine.org)
- Running the modified TWINSCAN, on both the human and fruit fly genomes, Brent and colleagues predicted about 25,000 transcription-start sites, compared with a known 6,000. (bio-medicine.org)
- On average one nucleotide position per thousand (1 per kb) is different when two individual genomes are compared, although this figure is lower (approximately 1 per 2 kb) in protein coding sequence. (sanger.ac.uk)
- Activation of aberrant 5' cleavage sites involves base pairing between U5 snRNA and nucleotides upstream of the cleavage site. (nih.gov)
- Aberrant splice sites. (genecards.org)
- These aberrant splicing patterns were not observed when wild type sequence was used for the assay. (aacrjournals.org)
- The variant led to an aberrant splicing resulting in an in-frame 33-bp insertion, which caused an 11-amino acid insertion in the presumptive cytoplasmic loop. (unboundmedicine.com)
- Targeted capture and massively parallel sequencing of 12 human exomes. (nih.gov)
- Here we report on the targeted capture and massively parallel sequencing of the exomes of 12 humans. (nih.gov)
- To address the underlying genetics, we analyzed 48 SI-NETs by massively parallel exome sequencing. (cancerindex.org)
- ALEXA-Seq - alternative expression analysis by massively parallel sequencing. (github.com)
- We tested this hypothesis using massively parallel sequencing of DNA from Proteus syndrome tissues, comparing affected to unaffected tissues. (genome.gov)
- Berget SM (1995) Exon recognition in vertebrate splicing. (springer.com)
- We show that IVS1-6A/T (−23 Hph I+/−) is a key INS variant that influences alternative splicing of intron 1 through differential recognition of its 3′ splice site. (diabetesjournals.org)
- IVS1-6A/T is located in the polypyrimidine tract (PPT), a splicing signal of central importance for vertebrate 3′ splice site recognition, and in a position exhibiting a great depletion of purine residues in the PPT ( 8 ). (diabetesjournals.org)
- To test whether the IVS1-6A→T base change promotes PPT recognition and splicing of intron 1, we transiently transfected the wild-type and mutated INS minigenes ( Fig. 1 A ) into several cell lines and examined their splicing pattern. (diabetesjournals.org)
- In this work, we propose two transfer learning approaches for the splice site recognition problem, which take into account the knowledge we have from the well-studied organisms. (demokritos.gr)
- These results can be used in sequence annotation. (scirp.org)
- M. Nowrousian, C. Würtz, S. P?ggeler, and U. Kück, (2004) Comparative sequence analysis of Sordaria macrospora and Neurospora crassa as a means to improve genome annotation, Fungal Genetics and Biology, 41, 285-292. (scirp.org)
- 3. 3 Genome Sequencing Project Introduction Assembly Automated Annotation Manual annotation Using Web Apollo Merge: automated + manual Genome-wide & gene- specific comparative analyses QC QC Synthesis & dissemination. (slideshare.net)
- In this study, we present the annotation of the first whole-genome shotgun assembly of loblolly pine ( Pinus taeda L.), which comprises 20.1 Gb of sequence. (genetics.org)
- Next we'll add the annotation tracks ids for the genomic sequences for our organism. (gmod.org)
- Now that we have an user created and the annotation track ids loaded, we'll need to give the user permissions to access the sequence. (gmod.org)
- outrigger - calculate alternative splicing scores of RNA-Seq data based on junction reads and a de novo, custom annotation created with a graph database, especially made for single-cell analyses. (github.com)
- MAASE - Convenient access, identification, and annotation of alternative splicing events (ASEs), designed specifically with experimentalists in mind. (github.com)
- In addition, we show that a rare insertion/deletion polymorphism IVS1+5insTTGC ( IVS-69 ), which is exclusively present in Africans, activated a downstream cryptic 5′ splice site, extending the 5′ leader by 30 bp. (diabetesjournals.org)
- An additional probe 9C/TM (5′-TGCTTGGCGGCGCCTGGAA-3′) was used to detect splicing of the cryptic donor splice site in exon IIIc to the downstream transmembrane exon 11. (bmj.com)
- Light-induced AS from a downstream 3′ splice site gives rise to SR30.1 , which is exported to the cytosol and translated, coinciding with SR30 protein accumulation upon seedling illumination. (plantphysiol.org)
- Alternative 3' splice site (A3SS): An alternative 3' splice junction (acceptor site) is used that changes the 5' boundary of the downstream exon. (github.com)
- The active donor site sequences included a 9-nucleotide consensus sequence, 14- or 16-nucleotide sequences at the human beta-globin first or second donor, and those at simian virus 40 large T antigen or small t antigen donor. (asm.org)
- D-F ) Views of the penultimate dU2AF 65 -bound nucleotide including rU interactions (PDB ID code 2G4B) ( D ), which are indistinguishable from dU at this site, dA interactions ( E ), and dG interactions ( F ). (G) dU2AF 65 -D231V bound to the dUdUdUdU(5-Br-dU) dU dU. (pnas.org)
- An FCT is a discrete but not necessarily contiguous region of a gene that, by means of its nucleotide sequence, influences the production, processing, or biological activity of a particular nucleic acid or protein, or its specific binding to another molecule. (wordpress.com)
- The Foxo4 targeting vector contained 6.5 kb of genomic sequence immediately 5′ side of the first exon followed by a 1.3-kb phosphoglycerate kinase promoter-driven neomycin phosphotransferase (PGK-Neo) cassette and 1.5 kb of genomic sequence of intron 1. (pnas.org)
- A gene is a genomic sequence (DNA or RNA) directly encoding func'onal product molecules, either RNA or protein. (slideshare.net)
- We need to generate a file of genomic sequence ids for the script. (gmod.org)
- Let's first create the list of genomic sequence ids. (gmod.org)
- We'll need to provide the script a list of genomic sequence ids, like in the previous step. (gmod.org)
- the sequences used to determine where the splicing will occur. (bio.net)
- the type of splicing depends on the structure of the spliced intron and the catalysts required for splicing to occur. (wikipedia.org)
- The idea was to look at short sequences that occur many times in the genome. (healthcanal.com)
- Sequences that help splicing often occur close to splice sites. (healthcanal.com)
- There are several different alternative splicing modes that occur, and there are five basic modes that are most often recognized. (brighthub.com)
- A crosstalk between editing and splicing is likely to occur here. (wikipedia.org)
- Whole exome sequencing with confirmatory Sanger sequencing were performed for the two patients and healthy family members. (biomedcentral.com)
- Recently, there has been a shift towards applying broader exome and/or genome sequencing to interrogate more of the genome to provide a genetic diagnosis for cardiomyopathy. (mdpi.com)
- Seventeen samples from 11 patients were sequenced using targeted exome capture. (genome.gov)
- Four alternatively spliced forms of the slo -α gene from chick hair cells were co-expressed with accessory β subunits (from quail cochlea) by transient transfection of human embryonic kidney 293 cells. (jneurosci.org)
- It is possible, if we're willing to go through the trouble, to annotate the alternatively spliced forms of Aldolase from the other species, but I'm sacrificing thoroughness for the sake of accessibility. (scienceblogs.com)
- The transcriptome of the filamentous fungus Trichoderma longibrachiatum was deep sequenced using Illumina Solexa technology. (biomedcentral.com)
- This unexpectedly high ratio of alternative splicing suggests that alternative splicing is important to the transcriptome diversity of T. longibrachiatum . (biomedcentral.com)
- This study, consisting of a comprehensive analysis of the alternative splicing landscape in the filamentous fungus T. longibrachiatum , revealed an unexpectedly high ratio of alternative splicing events and provided new insights into transcriptome diversity in fungi. (biomedcentral.com)
- The application of high-throughput sequencing technologies to whole transcriptome sequencing (RNA-Seq) prompts our understanding of AS. (biomedcentral.com)
- In addition, flat file access to the FASTA sequences of the genome and transcriptome, annotations, and gff3 files are available through the database FTP site ( http://loblolly.ucdavis.edu/bipod/ftp/Genome_Data/genome/pinerefseq/Pita/ ). (genetics.org)
- Next generation sequencing technologies open exciting new possibilities for genome and transcriptome sequencing. (biomedcentral.com)
- H-DBAS - Human-transcriptome DataBase for Alternative Splicing. (github.com)
- The isolation, sequence and structural analysis of the human PEDF gene and its promoter along with its evolutionary conservation and expression in human tissues are now described. (molvis.org)
- The immediate 5'-flanking region is dominated by a dense cluster of Alu repeats in which are embedded several promoter consensus sequences. (molvis.org)
- These are known as multiple polyadenylation and multiple promoter sites. (brighthub.com)
- We used in silico sequence analysis, reverse-transcription PCR, quantitative PCR, and transient transfection assays of promoter function to define splice-site usage and the function of an internal promoter in mouse Inpp5b versus human INPP5B. (deepdyve.com)
- The promoter region of dshsp90 contained putative cis -acting stress responsive elements and binding sites of transcriptional factors that respond to heat shock and salt stress. (mdpi.com)
- FirstEF is designed to recognize CpG islands, promoter regions and first splice-donor sites. (the-scientist.com)
- Our algorithms were optimized and tested using artificially spliced genomic reads produced with the Illumina Genome Analyzer for the model plant Arabidopsis thaliana . (biomedcentral.com)
- We sequenced 2.2 Mb representing triplicated genome segments of Brassica oleracea , which are each paralogous with one another and homologous with a segmentally duplicated region of the Arabidopsis thaliana genome. (plantcell.org)
- flotilla - reproduce machine learning analysis of gene expression and alternative splicing data. (github.com)
- The recently found heterogeneity in isoform expression mechanisms in single cells [ 35 , 36 , 37 , 38 ] is highly intriguing to the scientific community, and raises the question of whether this diverse and complex isoform expression landscape constitutes an additional layer of gene expression regulation or is solely a result of the stochastic functioning of the alternative splicing machinery. (springer.com)
- Purine interruptions of polypyrimidine (Py) tract splice site signals contribute to human genetic diseases. (pnas.org)
- The graphic browser output displays the four core splicing signals with scores based on nine different algorithms and highlights sequences belonging to 13 different groups of SRSs. (pitt.edu)
- Some of the signals that regulate transcription reside right near the transcription site. (bio-medicine.org)
- Also referred to as cassette exon, this mode involves an exon that may be retained or spliced out of the primary transcript. (brighthub.com)
- We provide evidence that SR30.2 can be further spliced and, unlike SR30.2 , the resulting cassette exon variant SR30.3 is sensitive to nonsense-mediated decay. (plantphysiol.org)
- Skipped exon or cassette exon (SE): An exon can be retained or spliced out of the primary transcript. (github.com)
- I have not included the 'consensus' branch point sequence because it is just too degenerate for me to believe it completely. (bio.net)
- and branch site (TCCTRAY). (umd.edu)
- and the polypyrimidine tract (which is thought to recruit factors to the branch point sequence and 3′ splice site). (evolutionnews.org)
- The branch point sequence is identified and bound by the branch-point-binding protein (BBP). (evolutionnews.org)
- The first transesterification reaction then takes place, and a cut is made at the 5′ splice site and the 5′ end of the intron is subsequently connected to the conserved adenine found in the branch point sequence, forming the so-called "lariat" structure. (evolutionnews.org)
- All had consensus splice and branch site sequences ( 16 ). (sciencemag.org)
- This phenomenon was evident in the earliest observations of alternative splicing using chromatin spreads of the Drosophila chorion gene. (springer.com)
- Our training and test sets of human and Drosophila melanogaster splice sites are available to the community for testing splice site predictors. (fruitfly.org)
- V. Brendal, L. Xing, and W. Zhu, (2004) Gene structure pre-diction from consensus spliced alignment of multiple ESTs matching the same genomic locus, Bioinformatics, 20, 1157-1169. (scirp.org)
- He also helped the EU-SOL project with the bioinformatics support of the international effort to sequence the tomato genome. (routledge.com)