RNA-Binding Proteins: Proteins that bind to RNA molecules. Included here are RIBONUCLEOPROTEINS and other proteins whose function is to bind specifically to RNA.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)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).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.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.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, Viral: Ribonucleic acid that makes up the genetic material of viruses.Hu Paraneoplastic Encephalomyelitis Antigens: A family of RNA-binding proteins that are homologues of ELAV protein, Drosophila. They were initially identified in humans as the targets of autoantibodies in patients with PARANEOPLASTIC ENCEPHALOMYELITIS. They are thought to regulate GENE EXPRESSION at the post-transcriptional level.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.RNA Stability: The extent to which an RNA molecule retains its structural integrity and resists degradation by RNASE, and base-catalyzed HYDROLYSIS, under changing in vivo or in vitro conditions.RNA Splicing: The ultimate exclusion of nonsense sequences or intervening sequences (introns) before the final RNA transcript is sent to the cytoplasm.Base Sequence: The sequence of PURINES and PYRIMIDINES in nucleic acids and polynucleotides. It is also called nucleotide sequence.RNA, Small Interfering: Small double-stranded, non-protein coding RNAs (21-31 nucleotides) involved in GENE SILENCING functions, especially RNA INTERFERENCE (RNAi). Endogenously, siRNAs are generated from dsRNAs (RNA, DOUBLE-STRANDED) by the same ribonuclease, Dicer, that generates miRNAs (MICRORNAS). The perfect match of the siRNAs' antisense strand to their target RNAs mediates RNAi by siRNA-guided RNA cleavage. siRNAs fall into different classes including trans-acting siRNA (tasiRNA), repeat-associated RNA (rasiRNA), small-scan RNA (scnRNA), and Piwi protein-interacting RNA (piRNA) and have different specific gene silencing functions.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, Double-Stranded: RNA consisting of two strands as opposed to the more prevalent single-stranded RNA. Most of the double-stranded segments are formed from transcription of DNA by intramolecular base-pairing of inverted complementary sequences separated by a single-stranded loop. Some double-stranded segments of RNA are normal in all organisms.RNA Editing: A process that changes the nucleotide sequence of mRNA from that of the DNA template encoding it. Some major classes of RNA editing are as follows: 1, the conversion of cytosine to uracil in mRNA; 2, the addition of variable number of guanines at pre-determined sites; and 3, the addition and deletion of uracils, templated by guide-RNAs (RNA, GUIDE).Binding Sites: The parts of a macromolecule that directly participate in its specific combination with another molecule.Nuclear Factor 90 Proteins: A family of double-stranded RNA-binding proteins that are related to NFATC TRANSCRIPTION FACTORS. In addition to binding to RNA, nuclear factor 90 proteins form heterodimeric complexes that regulate GENETIC TRANSCRIPTION and may play a role in T-CELL activation.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.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.RNA, Bacterial: Ribonucleic acid in bacteria having regulatory and catalytic roles as well as involvement in protein synthesis.RNA, Ribosomal: The most abundant form of RNA. Together with proteins, it forms the ribosomes, playing a structural role and also a role in ribosomal binding of mRNA and tRNAs. Individual chains are conventionally designated by their sedimentation coefficients. In eukaryotes, four large chains exist, synthesized in the nucleolus and constituting about 50% of the ribosome. (Dorland, 28th ed)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.RNA Interference: A gene silencing phenomenon whereby specific dsRNAs (RNA, DOUBLE-STRANDED) trigger the degradation of homologous mRNA (RNA, MESSENGER). The specific dsRNAs are processed into SMALL INTERFERING RNA (siRNA) which serves as a guide for cleavage of the homologous mRNA in the RNA-INDUCED SILENCING COMPLEX. DNA METHYLATION may also be triggered during this process.RNA 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.Nucleic Acid Conformation: The spatial arrangement of the atoms of a nucleic acid or polynucleotide that results in its characteristic 3-dimensional shape.Carrier Proteins: Transport proteins that carry specific substances in the blood or across cell membranes.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.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.Nuclear Factor 45 Protein: A protein subunit that takes part in forming nuclear factor 90 protein complexes.RNA Helicases: A family of proteins that promote unwinding of RNA during splicing and translation.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.Protein Biosynthesis: The biosynthesis of PEPTIDES and PROTEINS on RIBOSOMES, directed by MESSENGER RNA, via TRANSFER RNA that is charged with standard proteinogenic AMINO ACIDS.RNA, Fungal: Ribonucleic acid in fungi having regulatory and catalytic roles as well as involvement in protein synthesis.Heterogeneous-Nuclear Ribonucleoprotein D: A heterogeneous-nuclear ribonucleoprotein that has specificity for AU-rich elements found in the 3'-region of mRNA and may play a role in RNA stability. Several isoforms of hnRNP D protein have been found to occur due to alternative mRNA splicing (RNA SPLICING).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.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-Binding Protein FUS: A multifunctional heterogeneous-nuclear ribonucleoprotein that may play a role in homologous DNA pairing and recombination. The N-terminal portion of protein is a potent transcriptional activator, while the C terminus is required for RNA binding. The name FUS refers to the fact that genetic recombination events result in fusion oncogene proteins (ONCOGENE PROTEINS, FUSION) that contain the N-terminal region of this protein. These fusion proteins have been found in myxoid liposarcoma (LIPOSARCOMA, MYXOID) and acute myeloid leukemia.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.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)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.RNA, Protozoan: Ribonucleic acid in protozoa having regulatory and catalytic roles as well as involvement in protein synthesis.RNA, Chloroplast: Ribonucleic acid in chloroplasts having regulatory and catalytic roles as well as involvement in protein synthesis.Cell Line: Established cell cultures that have the potential to propagate indefinitely.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.RNA, Plant: Ribonucleic acid in plants having regulatory and catalytic roles as well as involvement in protein synthesis.mRNA Cleavage and Polyadenylation Factors: Factors that are involved in directing the cleavage and POLYADENYLATION of the of MESSENGER RNA near the site of the RNA 3' POLYADENYLATION SIGNALS.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.DNA-Directed RNA Polymerases: Enzymes that catalyze DNA template-directed extension of the 3'-end of an RNA strand one nucleotide at a time. They can initiate a chain de novo. In eukaryotes, three forms of the enzyme have been distinguished on the basis of sensitivity to alpha-amanitin, and the type of RNA synthesized. (From Enzyme Nomenclature, 1992).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.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.Cytoplasm: The part of a cell that contains the CYTOSOL and small structures excluding the CELL NUCLEUS; MITOCHONDRIA; and large VACUOLES. (Glick, Glossary of Biochemistry and Molecular Biology, 1990)Host Factor 1 Protein: An integration host factor that was originally identified as a bacterial protein required for the integration of bacteriophage Q beta (ALLOLEVIVIRUS). Its cellular function may be to regulate mRNA stability and processing in that it binds tightly to poly(A) RNA and interferes with ribosome binding.Models, Molecular: Models used experimentally or theoretically to study molecular shape, electronic properties, or interactions; includes analogous molecules, computer-generated graphics, and mechanical structures.Transcription Factors: Endogenous substances, usually proteins, which are effective in the initiation, stimulation, or termination of the genetic transcription process.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.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.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.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.Amino Acid Motifs: Commonly observed structural components of proteins formed by simple combinations of adjacent secondary structures. A commonly observed structure may be composed of a CONSERVED SEQUENCE which can be represented by a CONSENSUS SEQUENCE.RNA Viruses: Viruses whose genetic material is RNA.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.Recombinant Fusion Proteins: Recombinant proteins produced by the GENETIC TRANSLATION of fused genes formed by the combination of NUCLEIC ACID REGULATORY SEQUENCES of one or more genes with the protein coding sequences of one or more genes.Heterogeneous-Nuclear Ribonucleoprotein Group C: A group of closely related heterogeneous-nuclear ribonucleoproteins of approximately 41-43 kDa in size found in the cell nucleus. Members of this class have been implicated in a variety of processes including splicing, polyadenylation, and nuclear retention of RNA.RNA, Untranslated: RNA which does not code for protein but has some enzymatic, structural or regulatory function. Although ribosomal RNA (RNA, RIBOSOMAL) and transfer RNA (RNA, TRANSFER) are also untranslated RNAs they are not included in this scope.RNA Transport: The process of moving specific RNA molecules from one cellular compartment or region to another by various sorting and transport mechanisms.RNA, Nuclear: RNA molecules found in the nucleus either associated with chromosomes or in the nucleoplasm.Recombinant Proteins: Proteins prepared by recombinant DNA technology.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.Poly(A)-Binding Protein I: A poly(A) binding protein that has a variety of functions such as mRNA stabilization and protection of RNA from nuclease activity. Although poly(A) binding protein I is considered a major cytoplasmic RNA-binding protein it is also found in the CELL NUCLEUS and may be involved in transport of mRNP particles.Tacrolimus Binding Proteins: A family of immunophilin proteins that bind to the immunosuppressive drugs TACROLIMUS (also known as FK506) and SIROLIMUS. EC 5.2.1.-RNA, Guide: Small kinetoplastid mitochondrial RNA that plays a major role in RNA EDITING. These molecules form perfect hybrids with edited mRNA sequences and possess nucleotide sequences at their 5'-ends that are complementary to the sequences of the mRNA's immediately downstream of the pre-edited regions.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.Ribonuclease III: An endoribonuclease that is specific for double-stranded RNA. It plays a role in POST-TRANSCRIPTIONAL RNA PROCESSING of pre-RIBOSOMAL RNA and a variety of other RNA structures that contain double-stranded regions.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.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.RNA Polymerase II: A DNA-dependent RNA polymerase present in bacterial, plant, and animal cells. It functions in the nucleoplasmic structure and transcribes DNA into RNA. It has different requirements for cations and salt than RNA polymerase I and is strongly inhibited by alpha-amanitin. EC 2.7.7.6.Nucleocytoplasmic Transport Proteins: Proteins involved in the process of transporting molecules in and out the cell nucleus. Included here are: NUCLEOPORINS, which are membrane proteins that form the NUCLEAR PORE COMPLEX; KARYOPHERINS, which carry molecules through the nuclear pore complex; and proteins that play a direct role in the transport of karyopherin complexes through the nuclear pore complex.Sequence Analysis, RNA: A multistage process that includes cloning, physical mapping, subcloning, sequencing, and information analysis of an RNA SEQUENCE.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.Two-Hybrid System Techniques: Screening techniques first developed in yeast to identify genes encoding interacting proteins. Variations are used to evaluate interplay between proteins and other molecules. Two-hybrid techniques refer to analysis for protein-protein interactions, one-hybrid for DNA-protein interactions, three-hybrid interactions for RNA-protein interactions or ligand-based interactions. Reverse n-hybrid techniques refer to analysis for mutations or other small molecules that dissociate known interactions.Tristetraprolin: A ZINC FINGER MOTIF containing transcription factor that was originally identified as one of the IMMEDIATE-EARLY PROTEINS. It shuttles between the CYTOPLASM and the CELL NUCLEUS and is involved in destabilization of mRNAs for TUMOR NECROSIS FACTOR-ALPHA.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.Iron-Regulatory Proteins: Proteins that regulate cellular and organismal iron homeostasis. They play an important biological role by maintaining iron levels that are adequate for metabolic need, but below the toxicity threshold.Repressor Proteins: Proteins which maintain the transcriptional quiescence of specific GENES or OPERONS. Classical repressor proteins are DNA-binding proteins that are normally bound to the OPERATOR REGION of an operon, or the ENHANCER SEQUENCES of a gene until a signal occurs that causes their release.Nerve Tissue ProteinsOligoribonucleotides: A group of ribonucleotides (up to 12) in which the phosphate residues of each ribonucleotide act as bridges in forming diester linkages between the ribose moieties.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.Saccharomyces cerevisiae Proteins: Proteins obtained from the species SACCHAROMYCES CEREVISIAE. The function of specific proteins from this organism are the subject of intense scientific interest and have been used to derive basic understanding of the functioning similar proteins in higher eukaryotes.Regulatory Sequences, Ribonucleic Acid: Sequences within RNA that regulate the processing, stability (RNA STABILITY) or translation (TRANSLATION, GENETIC) of RNA.RNA Caps: Nucleic acid structures found on the 5' end of eukaryotic cellular and viral messenger RNA and some heterogeneous nuclear RNAs. These structures, which are positively charged, protect the above specified RNAs at their termini against attack by phosphatases and other nucleases and promote mRNA function at the level of initiation of translation. Analogs of the RNA caps (RNA CAP ANALOGS), which lack the positive charge, inhibit the initiation of protein synthesis.Ribosomal Proteins: Proteins found in ribosomes. They are believed to have a catalytic function in reconstituting biologically active ribosomal subunits.RNA Folding: The processes of RNA tertiary structure formation.RNA, Antisense: RNA molecules which hybridize to complementary sequences in either RNA or DNA altering the function of the latter. Endogenous antisense RNAs function as regulators of gene expression by a variety of mechanisms. Synthetic antisense RNAs are used to effect the functioning of specific genes for investigative or therapeutic purposes.Insulin-Like Growth Factor Binding Proteins: A family of soluble proteins that bind insulin-like growth factors and modulate their biological actions at the cellular level. (Int J Gynaecol Obstet 1992;39(1):3-9)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.Blotting, Western: Identification of proteins or peptides that have been electrophoretically separated by blot transferring from the electrophoresis gel to strips of nitrocellulose paper, followed by labeling with antibody probes.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.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.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.Immunoprecipitation: The aggregation of soluble ANTIGENS with ANTIBODIES, alone or with antibody binding factors such as ANTI-ANTIBODIES or STAPHYLOCOCCAL PROTEIN A, into complexes large enough to fall out of solution.Fragile X Mental Retardation Protein: A RNA-binding protein that is found predominately in the CYTOPLASM. It helps regulate GENETIC TRANSLATION in NEURONS and is absent or under-expressed in FRAGILE X SYNDROME.Zinc Fingers: Motifs in DNA- and RNA-binding proteins whose amino acids are folded into a single structural unit around a zinc atom. In the classic zinc finger, one zinc atom is bound to two cysteines and two histidines. In between the cysteines and histidines are 12 residues which form a DNA binding fingertip. By variations in the composition of the sequences in the fingertip and the number and spacing of tandem repeats of the motif, zinc fingers can form a large number of different sequence specific binding sites.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.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.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).RNA, Transfer: The small RNA molecules, 73-80 nucleotides long, that function during translation (TRANSLATION, GENETIC) to align AMINO ACIDS at the RIBOSOMES in a sequence determined by the mRNA (RNA, MESSENGER). There are about 30 different transfer RNAs. Each recognizes a specific CODON set on the mRNA through its own ANTICODON and as aminoacyl tRNAs (RNA, TRANSFER, AMINO ACYL), each carries a specific amino acid to the ribosome to add to the elongating peptide chains.Sequence Deletion: Deletion of sequences of nucleic acids from the genetic material of an individual.RNA, Helminth: Ribonucleic acid in helminths having regulatory and catalytic roles as well as involvement in protein synthesis.Bacterial Proteins: Proteins found in any species of bacterium.Xenopus Proteins: Proteins obtained from various species of Xenopus. Included here are proteins from the African clawed frog (XENOPUS LAEVIS). Many of these proteins have been the subject of scientific investigations in the area of MORPHOGENESIS and development.Protein Isoforms: Different forms of a protein that may be produced from different GENES, or from the same gene by ALTERNATIVE SPLICING.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.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).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).Arabidopsis Proteins: Proteins that originate from plants species belonging to the genus ARABIDOPSIS. The most intensely studied species of Arabidopsis, Arabidopsis thaliana, is commonly used in laboratory experiments.Molecular Weight: The sum of the weight of all the atoms in a molecule.Polyribosomes: A multiribosomal structure representing a linear array of RIBOSOMES held together by messenger RNA; (RNA, MESSENGER); They represent the active complexes in cellular protein synthesis and are able to incorporate amino acids into polypeptides both in vivo and in vitro. (From Rieger et al., Glossary of Genetics: Classical and Molecular, 5th ed)Drosophila melanogaster: A species of fruit fly much used in genetics because of the large size of its chromosomes.Kinetics: The rate dynamics in chemical or physical systems.Trypanosoma brucei brucei: A hemoflagellate subspecies of parasitic protozoa that causes nagana in domestic and game animals in Africa. It apparently does not infect humans. It is transmitted by bites of tsetse flies (Glossina).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.Electrophoretic Mobility Shift Assay: An electrophoretic technique for assaying the binding of one compound to another. Typically one compound is labeled to follow its mobility during electrophoresis. If the labeled compound is bound by the other compound, then the mobility of the labeled compound through the electrophoretic medium will be retarded.MicroRNAs: Small double-stranded, non-protein coding RNAs, 21-25 nucleotides in length generated from single-stranded microRNA gene transcripts by the same RIBONUCLEASE III, Dicer, that produces small interfering RNAs (RNA, SMALL INTERFERING). They become part of the RNA-INDUCED SILENCING COMPLEX and repress the translation (TRANSLATION, GENETIC) of target RNA by binding to homologous 3'UTR region as an imperfect match. The small temporal RNAs (stRNAs), let-7 and lin-4, from C. elegans, are the first 2 miRNAs discovered, and are from a class of miRNAs involved in developmental timing.Gene Expression: The phenotypic manifestation of a gene or genes by the processes of GENETIC TRANSCRIPTION and GENETIC TRANSLATION.Ribosomes: Multicomponent ribonucleoprotein structures found in the CYTOPLASM of all cells, and in MITOCHONDRIA, and PLASTIDS. They function in PROTEIN BIOSYNTHESIS via GENETIC TRANSLATION.Mutagenesis, Site-Directed: Genetically engineered MUTAGENESIS at a specific site in the DNA molecule that introduces a base substitution, or an insertion or deletion.Crystallography, X-Ray: The study of crystal structure using X-RAY DIFFRACTION techniques. (McGraw-Hill Dictionary of Scientific and Technical Terms, 4th ed)Cells, Cultured: Cells propagated in vitro in special media conducive to their growth. Cultured cells are used to study developmental, morphologic, metabolic, physiologic, and genetic processes, among others.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.Fatty Acid-Binding Proteins: Intracellular proteins that reversibly bind hydrophobic ligands including: saturated and unsaturated FATTY ACIDS; EICOSANOIDS; and RETINOIDS. They are considered a highly conserved and ubiquitously expressed family of proteins that may play a role in the metabolism of LIPIDS.Ribonucleases: Enzymes that catalyze the hydrolysis of ester bonds within RNA. EC 3.1.-.Viral Proteins: Proteins found in any species of virus.Plant Proteins: Proteins found in plants (flowers, herbs, shrubs, trees, etc.). The concept does not include proteins found in vegetables for which VEGETABLE PROTEINS is available.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.Escherichia coli Proteins: Proteins obtained from ESCHERICHIA COLI.Models, Biological: Theoretical representations that simulate the behavior or activity of biological processes or diseases. For disease models in living animals, DISEASE MODELS, ANIMAL is available. Biological models include the use of mathematical equations, computers, and other electronic equipment.Protozoan Proteins: Proteins found in any species of protozoan.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.Arabidopsis: A plant genus of the family BRASSICACEAE that contains ARABIDOPSIS PROTEINS and MADS DOMAIN PROTEINS. The species A. thaliana is used for experiments in classical plant genetics as well as molecular genetic studies in plant physiology, biochemistry, and development.Phosphorylation: The introduction of a phosphoryl group into a compound through the formation of an ester bond between the compound and a phosphorus moiety.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.Protein Transport: The process of moving proteins from one cellular compartment (including extracellular) to another by various sorting and transport mechanisms such as gated transport, protein translocation, and vesicular transport.Active Transport, Cell Nucleus: Gated transport mechanisms by which proteins or RNA are moved across the NUCLEAR MEMBRANE.Genes, Reporter: Genes whose expression is easily detectable and therefore used to study promoter activity at many positions in a target genome. In recombinant DNA technology, these genes may be attached to a promoter region of interest.HEK293 Cells: A cell line generated from human embryonic kidney cells that were transformed with human adenovirus type 5.Substrate Specificity: A characteristic feature of enzyme activity in relation to the kind of substrate on which the enzyme or catalytic molecule reacts.Gene Expression Regulation, Developmental: Any of the processes by which nuclear, cytoplasmic, or intercellular factors influence the differential control of gene action during the developmental stages of an organism.Drosophila: A genus of small, two-winged flies containing approximately 900 described species. These organisms are the most extensively studied of all genera from the standpoint of genetics and cytology.Caenorhabditis elegans Proteins: Proteins from the nematode species CAENORHABDITIS ELEGANS. The proteins from this species are the subject of scientific interest in the area of multicellular organism MORPHOGENESIS.Poly(A)-Binding Protein II: A poly(A) binding protein that is involved in promoting the extension of the poly A tails of MRNA. The protein requires a minimum of ten ADENOSINE nucleotides in order for binding to mRNA. Once bound it works in conjunction with CLEAVAGE AND POLYADENYLATION SPECIFICITY FACTOR to stimulate the rate of poly A synthesis by POLY A POLYMERASE. Once poly-A tails reach around 250 nucleotides in length poly(A) binding protein II no longer stimulates POLYADENYLATION. Mutations within a GCG repeat region in the gene for poly(A) binding protein II have been shown to cause the disease MUSCULAR DYSTROPHY, OCULOPHARYNGEAL.Phenotype: The outward appearance of the individual. It is the product of interactions between genes, and between the GENOTYPE and the environment.Gene Expression Profiling: The determination of the pattern of genes expressed at the level of GENETIC TRANSCRIPTION, under specific circumstances or in a specific cell.Antigens, Surface: Antigens on surfaces of cells, including infectious or foreign cells or viruses. They are usually protein-containing groups on cell membranes or walls and may be isolated.Green Fluorescent Proteins: Protein analogs and derivatives of the Aequorea victoria green fluorescent protein that emit light (FLUORESCENCE) when excited with ULTRAVIOLET RAYS. They are used in REPORTER GENES in doing GENETIC TECHNIQUES. Numerous mutants have been made to emit other colors or be sensitive to pH.Caenorhabditis elegans: A species of nematode that is widely used in biological, biochemical, and genetic studies.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.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.eIF-2 Kinase: A dsRNA-activated cAMP-independent protein serine/threonine kinase that is induced by interferon. In the presence of dsRNA and ATP, the kinase autophosphorylates on several serine and threonine residues. The phosphorylated enzyme catalyzes the phosphorylation of the alpha subunit of EUKARYOTIC INITIATION FACTOR-2, leading to the inhibition of protein synthesis.Ultraviolet Rays: That portion of the electromagnetic spectrum immediately below the visible range and extending into the x-ray frequencies. The longer wavelengths (near-UV or biotic or vital rays) are necessary for the endogenous synthesis of vitamin D and are also called antirachitic rays; the shorter, ionizing wavelengths (far-UV or abiotic or extravital rays) are viricidal, bactericidal, mutagenic, and carcinogenic and are used as disinfectants.Cell Line, Tumor: A cell line derived from cultured tumor cells.Proteins: Linear POLYPEPTIDES that are synthesized on RIBOSOMES and may be further modified, crosslinked, cleaved, or assembled into complex proteins with several subunits. The specific sequence of AMINO ACIDS determines the shape the polypeptide will take, during PROTEIN FOLDING, and the function of the protein.Gene Expression Regulation, Viral: Any of the processes by which cytoplasmic factors influence the differential control of gene action in viruses.Argonaute Proteins: A family of RNA-binding proteins that has specificity for MICRORNAS and SMALL INTERFERING RNA molecules. The proteins take part in RNA processing events as core components of RNA-induced silencing complex.Karyopherins: A family of proteins involved in NUCLEOCYTOPLASMIC TRANSPORT. Karyopherins are heteromeric molecules composed two major types of components, ALPHA KARYOPHERINS and BETA KARYOPHERINS, that function together to transport molecules through the NUCLEAR PORE COMPLEX. Several other proteins such as RAN GTP BINDING PROTEIN and CELLULAR APOPTOSIS SUSCEPTIBILITY PROTEIN bind to karyopherins and participate in the transport process.Insulin-Like Growth Factor Binding Protein 3: One of the six homologous soluble proteins that bind insulin-like growth factors (SOMATOMEDINS) and modulate their mitogenic and metabolic actions at the cellular level.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.Fungal Proteins: Proteins found in any species of fungus.Gene Expression Regulation, Plant: Any of the processes by which nuclear, cytoplasmic, or intercellular factors influence the differential control of gene action in plants.Trans-Activators: Diffusible gene products that act on homologous or heterologous molecules of viral or cellular DNA to regulate the expression of proteins.Signal Transduction: The intracellular transfer of information (biological activation/inhibition) through a signal pathway. In each signal transduction system, an activation/inhibition signal from a biologically active molecule (hormone, neurotransmitter) is mediated via the coupling of a receptor/enzyme to a second messenger system or to an ion channel. Signal transduction plays an important role in activating cellular functions, cell differentiation, and cell proliferation. Examples of signal transduction systems are the GAMMA-AMINOBUTYRIC ACID-postsynaptic receptor-calcium ion channel system, the receptor-mediated T-cell activation pathway, and the receptor-mediated activation of phospholipases. Those coupled to membrane depolarization or intracellular release of calcium include the receptor-mediated activation of cytotoxic functions in granulocytes and the synaptic potentiation of protein kinase activation. Some signal transduction pathways may be part of larger signal transduction pathways; for example, protein kinase activation is part of the platelet activation signal pathway.Periplasmic Binding Proteins: Periplasmic proteins that scavenge or sense diverse nutrients. In the bacterial environment they usually couple to transporters or chemotaxis receptors on the inner bacterial membrane.Calcium-Binding Proteins: Proteins to which calcium ions are bound. They can act as transport proteins, regulator proteins, or activator proteins. They typically contain EF HAND MOTIFS.Oogenesis: The process of germ cell development in the female from the primordial germ cells through OOGONIA to the mature haploid ova (OVUM).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.Electrophoresis, Polyacrylamide Gel: Electrophoresis in which a polyacrylamide gel is used as the diffusion medium.Gene Expression Regulation, Bacterial: Any of the processes by which cytoplasmic or intercellular factors influence the differential control of gene action in bacteria.RNA, Neoplasm: RNA present in neoplastic tissue.In Situ Hybridization: A technique that localizes specific nucleic acid sequences within intact chromosomes, eukaryotic cells, or bacterial cells through the use of specific nucleic acid-labeled probes.Cytoplasmic Granules: Condensed areas of cellular material that may be bounded by a membrane.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.Levivirus: A bacteriophage genus of the family LEVIVIRIDAE, whose viruses contain the short version of the genome and have a separate gene for cell lysis.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.Xenopus: An aquatic genus of the family, Pipidae, occurring in Africa and distinguished by having black horny claws on three inner hind toes.Gene Knockdown Techniques: The artificial induction of GENE SILENCING by the use of RNA INTERFERENCE to reduce the expression of a specific gene. It includes the use of DOUBLE-STRANDED RNA, such as SMALL INTERFERING RNA and RNA containing HAIRPIN LOOP SEQUENCE, and ANTI-SENSE OLIGONUCLEOTIDES.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.Oligonucleotide Array Sequence Analysis: Hybridization of a nucleic acid sample to a very large set of OLIGONUCLEOTIDE PROBES, which have been attached individually in columns and rows to a solid support, to determine a BASE SEQUENCE, or to detect variations in a gene sequence, GENE EXPRESSION, or for GENE MAPPING.Adaptor Proteins, Signal Transducing: A broad category of carrier proteins that play a role in SIGNAL TRANSDUCTION. They generally contain several modular domains, each of which having its own binding activity, and act by forming complexes with other intracellular-signaling molecules. Signal-transducing adaptor proteins lack enzyme activity, however their activity can be modulated by other signal-transducing enzymesOocytes: Female germ cells derived from OOGONIA and termed OOCYTES when they enter MEIOSIS. The primary oocytes begin meiosis but are arrested at the diplotene state until OVULATION at PUBERTY to give rise to haploid secondary oocytes or ova (OVUM).Down-Regulation: A negative regulatory effect on physiological processes at the molecular, cellular, or systemic level. At the molecular level, the major regulatory sites include membrane receptors, genes (GENE EXPRESSION REGULATION), mRNAs (RNA, MESSENGER), and proteins.TATA-Box Binding Protein: A general transcription factor that plays a major role in the activation of eukaryotic genes transcribed by RNA POLYMERASES. It binds specifically to the TATA BOX promoter element, which lies close to the position of transcription initiation in RNA transcribed by RNA POLYMERASE II. Although considered a principal component of TRANSCRIPTION FACTOR TFIID it also takes part in general transcription factor complexes involved in RNA POLYMERASE I and RNA POLYMERASE III transcription.Tacrolimus Binding Protein 1A: A 12-KDa tacrolimus binding protein that is found associated with and may modulate the function of calcium release channels. It is a peptidyl-prolyl cis/trans isomerase which is inhibited by both tacrolimus (commonly called FK506) and SIROLIMUS.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.Latent TGF-beta Binding Proteins: A family of secreted multidomain proteins that were originally identified by their association with the latent form of TRANSFORMING GROWTH FACTORS. They interact with a variety of EXTRACELLULAR MATRIX PROTEINS and may play a role in the regulation of TGB-beta bioavailability.Chlamydomonas reinhardtii: A species of GREEN ALGAE. Delicate, hairlike appendages arise from the flagellar surface in these organisms.Cell Differentiation: Progressive restriction of the developmental potential and increasing specialization of function that leads to the formation of specialized cells, tissues, and organs.Protein Structure, Secondary: The level of protein structure in which regular hydrogen-bond interactions within contiguous stretches of polypeptide chain give rise to alpha helices, beta strands (which align to form beta sheets) or other types of coils. This is the first folding level of protein conformation.Protein Interaction Mapping: Methods for determining interaction between PROTEINS.Binding, Competitive: The interaction of two or more substrates or ligands with the same binding site. The displacement of one by the other is used in quantitative and selective affinity measurements.Gene Silencing: Interruption or suppression of the expression of a gene at transcriptional or translational levels.
... RNA binding motif protein 33". Venter JC, Adams MD, Myers EW, et al. (2001). "The sequence of the human genome". Science ... RNA-binding protein 33 is a protein that in humans is encoded by the RBM33 gene. GRCh38: Ensembl release 89: ENSG00000184863 - ... 2004). "Sequence comparison of human and mouse genes reveals a homologous block structure in the promoter regions". Genome Res ... 2003). "The DNA sequence of human chromosome 7". Nature. 424 (6945): 157-64. doi:10.1038/nature01782. PMID 12853948. Ota T, ...
"Entrez Gene: RBM6 RNA binding motif protein 6". "OrthoMaM phylogenetic marker: RBM6 coding sequence". Güre AO, Altorki NK, ... RNA-binding protein 6 is a protein that in humans is encoded by the RBM6 gene. RBM6 orthologs have been identified in all ... 1999). "DEF-3(g16/NY-LU-12), an RNA binding protein from the 3p21.3 homozygous deletion region in SCLC". Oncogene. 18 (16): ... 2004). "Complete sequencing and characterization of 21,243 full-length human cDNAs". Nat. Genet. 36 (1): 40-5. doi:10.1038/ ...
Walia, R., El-Manzalawy, Y., Dobbs, D., and Honavar, V. (2017). Sequence-based Prediction of RNA-binding Residues in Proteins. ... analysis and prediction of protein-protein, protein-RNA, and protein-DNA interfaces and interactions, social network analytics ... Machine Learning and Sequence Homology-Based Methods to Improve the Reliability of Predicted RNA-Binding Residues in Proteins ... Towfic, F.; Caragea, C.; Dobbs, D.; Honavar, V. (2010). "Struct-NB: Predicting protein-RNA binding sites using structural ...
... sequence and characterization of a glycosylated RNA-binding protein". Nucleic Acids Research. 21 (18): 4210-7. doi:10.1093/nar/ ... "Entrez Gene: RBMX RNA binding motif protein, X-linked". Hofmann Y, Wirth B (Aug 2002). "hnRNP-G promotes exon 7 inclusion of ... a novel relative of SAM68 that interacts with an RNA-binding protein implicated in spermatogenesis". Human Molecular Genetics. ... Heterogeneous nuclear ribonucleoprotein G is a protein that in humans is encoded by the RBMX gene. This gene belongs to the ...
TATA-binding protein (TBP) can be recruited in two ways, by SAGA, a cofactor for RNA polymerase II, or by TFIID.[11] When ... For example, one study used the adenovirus TATA promoter sequence (5'-CGCTATAAAAGGGC-3') as a model binding sequence and found ... binds to the TATA box at its TATA-binding protein (TBP) subunit.[3] TBP binds to the minor groove[15] of the TATA box via a ... Transcription factors, TATA binding protein (TBP), and RNA polymerase II are all recruited to begin transcription. ...
Hohjoh, Hirohiko; Singer, Maxine F. (1997-10-01). "Sequence‐specific single‐strand RNA binding protein encoded by the human ... The specific RNA sequences that Singer produced were used to match each of the twenty amino acids to a specific RNA nucleotide ... These experiments also allowed them to create a library of artificial RNA strands of defined sequences, such as a molecule made ... They studied polynucleotide phosphorylase, an enzyme that can put together individual nucleotides into random RNA sequences. ...
Systems Biology of RNA Binding Proteins. Advances in Experimental Medicine and Biology 825. s. 431. ISBN 978-1-4939-1220-9. doi ... The C. elegans Sequencing Consortium (1998). «Genome Sequence of the Nematode C. Elegans: A Platform for Investigating Biology» ... Mellom anna vart mikro-RNA oppdaga i C. elegans i 1993.[8] ...
... that binds to RNA and inhibits prokaryotic protein synthesis and certain forms of RNA splicing. The gene cluster for viomycin ... Thomas, M.; Chan, Y.; Ozanick, S. (2003). "Deciphering tuberactinomycin biosynthesis: isolation, sequencing, and annotation of ... The tuberactinomycins target bacterial ribosomes, binding RNA and disrupting bacterial protein biosynthesis. It is produced by ... The NRPS contains 4 proteins: VioA, VioF, VioI, and VioG. These proteins condense and cyclize two molecules of L-2,3- ...
Pur-alpha (purα) is a sequence-specific single-stranded DNA and RNA-binding protein. Studies have shown that the protein is ... Recent studies have shown that mutations in phosphoinositide 3-kinase (PI3K) and AKT (also known as protein kinase B) pathway ... next step is to move to clinical trials involving humans in order to determine the exact genetic mutation causing the sequences ...
The encoded protein shows sequence similarity to the E. coli RNA polymerase-binding protein HepA. Mutations in this gene are a ... The SMARCAL1 protein convert RPA-bound, single stranded DNA into double-stranded DNA, an enzyme activity termed "annealing ... The protein encoded by this gene is a member of the SWI/SNF family of proteins. Members of this family have helicase and ATPase ... SWI/SNF-related matrix-associated actin-dependent regulator of chromatin subfamily A-like protein 1 is a protein that in humans ...
Heterogeneous nuclear ribonucleoprotein D0 (HNRNPD) also known as AU-rich element RNA-binding protein 1 (AUF1) is a protein ... The interaction sites on the RNA are frequently biased towards particular sequence motifs. These proteins are associated with ... The protein encoded by this gene has two repeats of quasi-RRM domains that bind to RNAs. It localizes to both the nucleus and ... "The UUAG-specific RNA binding protein, heterogeneous nuclear ribonucleoprotein D0. Common modular structure and binding ...
RNA-binding protein 25 is a protein that in humans is encoded by the RBM25 gene. GRCh38: Ensembl release 89: ENSG00000119707 - ... Ensembl, May 2017 "Human PubMed Reference:". "Toward a complete human genome sequence". Genome Res. 8 (11): 1097-108. Jan 1999 ... "Entrez Gene: RBM25 RNA binding motif protein 25". Elisei R, Weightman D, Kendall-Taylor P, Vassart G, Ludgate M (1993). "Muscle ... "Large-scale mapping of human protein-protein interactions by mass spectrometry". Mol. Syst. Biol. 3 (1): 89. doi:10.1038/ ...
The 15.5-kDa protein has sequence similarity to other RNA-binding proteins such as ribosomal proteins S12, L7a, and L30 and the ... "Entrez Gene: FBL fibrillarin". Protein-Protein and Protein-RNA Contacts both Contribute to the 15.5K-Mediated Assembly of the ... a central domain resembling other RNA-binding proteins and containing an RNP-2-like consensus sequence; and a C-terminal alpha- ... The 15.5-kDa protein also exists in a ribonucleoprotein complex that binds the U3 box B/C motif. The 15.5-kDa protein also ...
Promoters contain specific DNA sequences which give the RNA polymerase a place to bind. Other proteins also help this to happen ... This allows the RNA polymerase to bind with the promoter, and express the genes. The genes now synthesize lactase. Eventually, ... This stops the RNA polymerase from binding to the promoter and making lactase. Bottom: The gene is turned on. Lactose inhibits ... The promoter is recognized by RNA polymerase and another protein.. In eukaryotes. The process is more complicated. At least ...
Differential peak calling can also be applied in the context of analyzing RNA-binding protein binding sites. ChIP-sequencing ... When the protein is a transcription factor, the enriched area is its transcription factor binding site (TFBS). Popular software ... Meng, J.; Cui, X.; Rao, M. K.; Chen, Y.; Huang, Y. (14 April 2013). "Exome-based analysis for RNA epigenome sequencing data". ... Peak calling may be conducted on transcriptome/exome as well to RNA epigenome sequencing data from MeRIPseq or m6Aseq for ...
... can also recruit fusion proteins engineered to bind specific RNA sequences. Recruiting these proteins can allow ... Recruitment of endogenous or engineered RNA binding proteins for gene regulation[edit]. Endogenous proteins known to bind a ... Bridged activation: VP64 is fused to PP7, which recognizes and binds a sequence in the RNA module when the RNA module is ... Using a single construct with orthogonal RNA binding proteins where each protein is fused to a unique functional domain and ...
Experimental approaches have been used to define sequences that associate with specific RNA-binding proteins; specifically, ... "RNA Binding Protein/RNA Element Interactions and the Control of Translation". Current Protein & Peptide Science. 13 (4): 294- ... and membrane proteins. The poly(A) tail contains binding sites for poly(A) binding proteins (PABPs). These proteins cooperate ... The most common structure is a stem-loop, which provides a scaffold for RNA binding proteins and non-coding RNAs that influence ...
The ARM is a highly specific sequence which allows for the multimerization of Rev proteins, prior to RNA binding. A single base ... Rev initially binds to the purine-rich stem-loop IIB, then binds to a secondary site in stem-loop I. The RRE sequence is cis- ... The NLS overlaps with the sequence required for RNA-binding. This prevents the NLS from counteracting the export of RRE- ... The RRE also facilitates multimerization of the Rev proteins, which is required for Rev binding and function. The Rev protein ...
2007). "RNA-binding motif protein 15 binds to the RNA transport element RTE and provides a direct link to the NXF1 export ... 2004). "Complete sequencing and characterization of 21,243 full-length human cDNAs". Nat. Genet. 36 (1): 40-5. doi:10.1038/ ... Putative RNA-binding protein 15 is a protein that in humans is encoded by the RBM15 gene. GRCh38: Ensembl release 89: ... "Entrez Gene: RBM15 RNA binding motif protein 15". Strausberg RL, Feingold EA, Grouse LH, et al. (2003). "Generation and initial ...
RNA-binding protein 7 is a protein that in humans is encoded by the RBM7 gene. RBM7 has been shown to interact with SF3B2 and ... 2004). "Complete sequencing and characterization of 21,243 full-length human cDNAs". Nat. Genet. 36 (1): 40-5. doi:10.1038/ ... 2003). "Spermatogenetic expression of RNA-binding motif protein 7, a protein that interacts with splicing factors". J. Androl. ... "Spermatogenetic expression of RNA-binding motif protein 7, a protein that interacts with splicing factors". J. Androl. United ...
2007). "Nuclear translocation of the calcium-binding protein ALG-2 induced by the RNA-binding protein RBM22". Biochim. Biophys ... 2001). "Toward a Catalog of Human Genes and Proteins: Sequencing and Analysis of 500 Novel Complete Protein Coding Human cDNAs ... "Entrez Gene: RBM22 RNA binding motif protein 22". Loftus SK, Dixon J, Koprivnikar K, et al. (1996). "Transcriptional map of the ... 2001). "Systematic subcellular localization of novel proteins identified by large-scale cDNA sequencing". EMBO Rep. 1 (3): 287- ...
Pumilio homolog 2 is an RNA-binding protein that in humans is encoded by the PUM2 gene. BRCA1 has been shown to interact with ... Fox M, Urano J, Reijo Pera RA (2005). "Identification and characterization of RNA sequences to which human PUMILIO-2 (PUM2) and ... Nakayama M, Kikuno R, Ohara O (2003). "Protein-Protein Interactions Between Large Proteins: Two-Hybrid Screening Using a ... human members of the Pumilio family of RNA-binding proteins". Gene. 299 (1-2): 195-204. doi:10.1016/S0378-1119(02)01060-0. PMID ...
The encoded protein contains a sequence-specific RNA binding domain composed of eight repeats and N- and C-terminal flanking ... conserved RNA-binding proteins related to the Pumilio proteins of Drosophila and the fem-3 mRNA binding factor proteins of C. ... human members of the Pumilio family of RNA-binding proteins". Gene. 299 (1-2): 195-204. doi:10.1016/S0378-1119(02)01060-0. PMID ... "The PUF family of RNA-binding proteins: does evolutionarily conserved structure equal conserved function?". IUBMB Life. 55 (7 ...
This is frequently used in DNA/RNA binding protein studies, sequencing, and to prepare single stranded templates. Gene ... DNA/RNA or other molecule. There are three steps involved in the magnetic separation process: Bind - Microbeads bind to the ... The un-bound and un-wanted material that is left behind in the sample is removed by pipetting/aspiration. The bead-bound ... Proteins and protein complexes can be separated, e.g. in immunoprecipitation protocols. Molecular studies and diagnostics also ...
CLIP-Seq, a similar method for identifying the binding sites of cellular RNA-binding proteins (RBPs) or RNA modification sites ... The isolated RNA is converted into a cDNA library and is deep sequenced using next-generation sequencing technology. Recently, ... is a biochemical method for identifying the binding sites of cellular RNA-binding proteins (RBPs) and microRNA-containing ... A Method to Identify Transcriptome-wide the Binding Sites of RNA Binding Proteins". Journal of Visualized Experiments (41). doi ...
... sequence-specific DNA binding. • RNA polymerase II regulatory region sequence-specific DNA binding. • DNA binding. • sequence- ... Homeobox protein Hox-D8 is a protein that in humans is encoded by the HOXD8 gene.[5][6][7] ... transcriptional activator activity, RNA polymerase II transcription regulatory region sequence-specific binding. • RNA ... negative regulation of transcription from RNA polymerase II promoter. • positive regulation of transcription from RNA ...
... interaction between the iron-responsive element binding protein and its cognate rna is highly dependent upon both RNA sequence ... interaction between the iron-responsive element binding protein and its cognate rna is highly dependent upon both RNA sequence ... interaction between the iron-responsive element binding protein and its cognate rna is highly dependent upon both RNA sequence ... interaction between the iron-responsive element binding protein and its cognate rna is highly dependent upon both RNA sequence ...
LC sequence was shown to be both essential and sufficient for formation of RNA granules through trapping of RNA binding protein ... 1993). The protein product of the fragile X gene, FMR1, has characteristics of an RNA-binding protein. Cell 74, 291-298. doi: ... 1999). Biology of the fragile X mental retardation protein, an RNA-binding protein. Biochem. Cell Biol. 77, 331-342. doi: ... 1996). Specific sequences in the fragile X syndrome protein FMR1 and the FXR proteins mediate their binding to 60S ribosomal ...
Predicting the sequence specificities of DNA- and RNA-binding proteins by deep learning.. Alipanahi B1, Delong A2, Weirauch MT3 ... Knowing the sequence specificities of DNA- and RNA-binding proteins is essential for developing models of the regulatory ... that indicates how variations affect binding within a specific sequence. ... Here we show that sequence specificities can be ascertained from experimental data with deep learning techniques, which offer ...
The domain of the Bacillus subtilis DEAD-box helicase YxiN that is responsible for specific binding of 23S rRNA has an RNA ... Sequence Similarity Clusters for the Entities in PDB 2G0C Legend Entity #1 , Chains: A ATP-dependent RNA helicase dbpA protein ... Structure of the RNA binding domain (residues 404-479) of the Bacillus subtilis YxiN protein. ... Structures of protein chains with identical sequences (sequence identity > 95%) are aligned, superimposed and clustered. ...
The Ebola virus VP35 protein binds viral immunostimulatory and host RNAs identified through deep sequencing.. ... The Ebola virus VP35 protein binds viral immunostimulatory and host RNAs identified through deep sequencing.. ... The Ebola virus VP35 protein binds viral immunostimulatory and host RNAs identified through deep sequencing.. ... By deep sequencing the purified VP35-bound RNA, we identified the SeV copy-back defective interfering (DI) RNA, previously ...
... effects of binding sequences for the RNA polymerase α-subunit. N J Savery, V A Rhodius, H J Wing, S J W Busby ... effects of binding sequences for the RNA polymerase α-subunit Message Subject (Your Name) has forwarded a page to you from ... effects of binding sequences for the RNA polymerase α-subunit ... effects of binding sequences for the RNA polymerase α-subunit. ... An UP-element that can bind the C-terminal domain of the RNA polymerase (RNAP) alpha-subunit was cloned upstream of the DNA ...
BRAT was thought to be recruited to mRNAs indirectly through interaction with the RNA-binding protein Pumilio (PUM). However, ... analysis of the mRNAs associated with a TRIM-NHL protein and the first identification of an RNA motif bound by this protein ... it has recently been demonstrated that BRAT directly binds to RNA. The precise sequence recognized by BRAT, the extent of BRAT- ... BRAT binds mRNAs that encode proteins associated with a variety of functions, many of which are distinct from those implemented ...
... an SVM system was trained to recognize RNA-binding proteins. A total of 4011 RNA-binding and 9781 non-RNA-binding proteins was ... for the prediction of RNA-binding proteins directly from their primary sequence. Based on the knowledge of known RNA-binding ... RNA-binding proteins. RNA-protein interactions. rRNA. snRNA. Support vector machine. tRNA. ... Prediction of RNA-binding proteins from primary sequence by a support vector machine approach. RNA 10 (3) : 355-368. ...
RNA-binding motifs in proteins, and protein-binding recognition sites in RNA are provided. We emphasize sequence-based methods ... This chapter focuses on available computational methods for identifying which amino acids in an RNA-binding protein participate ... interfacial residues without the requirement for structural information regarding either the RNA-binding protein or its RNA ... but determining RNA-binding residues in proteins is still expensive and time-consuming. ...
R17 coat protein-R17 RNA, by T1 RNase yields an RNA fragment bound to the coat protein. The nucleotide sequence of this ... of RNA bacteriophage coat protein to 1 molecule of RNA represses in vitro translation of the RNA synthetase cistron. Digestion ... reveals that it contains the punctuation signal between the coat protein and RNA synthetase cistrons, suggesting that this is ... the site on the RNA where the coat protein acts as a translational repressor. ...
Users can perform simple and advanced searches based on annotations relating to sequence, structure and function. These ... The PDB archive contains information about experimentally-determined structures of proteins, nucleic acids, and complex ... Binds optimally to RNA containing 5-[AU]UAA-3 as a bipartite motif spaced by more than 15 nucleotides. Binds poly(A). RNA- ... RNA-binding protein that plays a role in the regulation of alternative splicing and influences mRNA splice site selection and ...
RNA splicing and processing, localization, stability and translation (Licatalosi and Darnell, 2010; McKee and Silver, 2007; ... RNA-binding proteins (RBPs) have a fundamental role in a wide variety of cellular processes including transcription, ... RNA-binding protein databases , Sequence analysis. RNA-binding proteins (RBPs) have a fundamental role in a wide variety of ... CISBP-RNA / Catalog of Inferred Sequence Binding Preferences of RNA binding proteins ...
The catalytic domain of an RNA-editing enzyme is fused with RNA-binding proteins. ... A New Way to ID Targets of RNA-Binding Proteins. By Ruth Williams , July 1, 2016 ... Scientists can now buy the direct-to-consumer sequencing product, and research participants can join 23andMes database. ...
walker: Sequence walkers: a graphical method to display how binding proteins interact with DNA or RNA sequences * @article{ ... a graphical method to display how binding proteins interact with {DNA} or {RNA} sequences", journal = "Nucleic Acids Res.", ... Sequence walkers at PubMed * Sequence walkers PDF for NAR version. Reproduced with permission from NAR Online, published by ... See also the companion paper: Information Content of Individual Genetic Sequences For more infomation see: Individual ...
A research team led by scientists at Boston University has identified several RNA-binding proteins as potential therapeutic ... This webinar will discuss novel long-read transcript sequencing (LRTseq) methods for transcriptome annotation that could ... BU Team IDs RNA-Binding Proteins as Potential Alzheimers Biomarkers. Jun 22, 2012 ... A research team led by scientists at Boston University has identified several RNA-binding proteins as potential therapeutic ...
NCBI Gene Model , MGI Sequence Detail. 148175. C57BL/6J. ± kb. transcript. NM_001357190. RefSeq , MGI Sequence Detail. 4139. ... J:31495 Abe R, et al., Tissue-specific expression of the gene encoding a mouse RNA binding protein homologous to human HuD ... protein coding gene. Chr4:110203722-110351911 (-). 129S1/SvImJ MGP_129S1SvImJ_G0028576. protein coding gene. Chr4:110997102- ... protein coding gene. Chr4:118772841-118925397 (-). DBA/2J MGP_DBA2J_G0028389. protein coding gene. Chr4:106625570-106779321 (-) ...
While there is evidence that distinct protein isoforms resulting from alternative pre-mRNA splicing play critical roles in ... Molecular Sequence Data * Motor Neurons / cytology * Phylogeny * RNA-Binding Proteins / genetics* * RNA-Binding Proteins / ... Two neuronal, nuclear-localized RNA binding proteins involved in synaptic transmission Curr Biol. 2003 Aug 5;13(15):1317-23. ... We show that unc-75 encodes an RRM domain-containing RNA binding protein that is exclusively expressed in the nervous system ...
The HBP protein as predicted by the cDNA sequence (Figure 3B) has no motifs in common with any known RNA binding or other ... The gene for histone RNA hairpin binding protein is located on human chromosome 4 and encodes a novel type of RNA binding ... that contains two binding sites for MS2 coat protein and a site for the RNA binding protein of interest (Figure 1B). The third ... The protein that binds the 3′ end of histone mRNA: a novel RNAbinding protein required for histone pre‐mRNA processing. Genes ...
... it is important to identify the DNA or RNA-binding residues in proteins. Protein sequence features, including the biochemical ... and it may not contain all the evolutionary information for modelling DNA or RNA-binding sites in protein sequences. In the ... descriptors of evolutionary information have been developed and evaluated for sequence-based prediction of DNA and RNA-binding ... specificity for RNA-binding site prediction. Predictions at this level of accuracy may provide useful information for modelling ...
Purchase High-Density Sequencing Applications in Microbial Molecular Genetics, Volume 612 - 1st Edition. Print Book. ISBN ... 6. Global recognition patterns of bacterial RNA-binding proteins. Erik Holmqvist. 7. High-resolution profiling of NMD targets. ... High-throughput analysis of protein-RNA and RNA-RNA interactions in pathogenic bacteria. Jai Tree. 20. Profiling RNA polymerase ... Addition sections cover Global recognition patterns of bacterial RNA-binding proteins, High-resolution profiling of NMD targets ...
... to survey the RNA associated with a panel of 24 chromatin regulators and traditional RNA binding proteins. For each protein ... For each protein, we find that the enriched sets of RNAs share distinct biochemical, functional, and chromatin properties. Thus ... that reproducibly bound measurable quantities of bulk RNA (90 % of the panel), we detect enrichment for hundreds to thousands ... However, it is unknown if these observations are specialized instances for a few key RNAs and chromatin factors in specific ...
Single Step Characterization of Regulatory Protein Binding Sites in RNA Using Phosphorothioates ... Exploring Sequence Space to Identify Binding Sites for Regulatory RNA-Binding Proteins, A Novel Saturation Mutagenesis ... Exploring Sequence Space to Identify Binding Sites for Regulatory RNA-Binding Proteins. Ravinder Singh1 ... Genome-wide Identification of Alternatively Spliced MRNA Targets of Specific RNA-binding Proteins PloS One. Jun, 2007 , Pubmed ...
Using RNA-sequencing to Detect Novel Splice Variants Related to Drug Resistance in In Vitro Cancer Models, A Rapid High- ... Real-time Analysis of Transcription Factor Binding, Transcription, Translation, and Turnover to Display Global Events During ... RNA Splicing, Engineering Artificial Factors to Specifically Manipulate Alternative Splicing in Human Cells, What is Gene ... Exploring Sequence Space to Identify Binding Sites for Regulatory RNA-Binding Proteins. Ravinder Singh1 ...
The Sources of Sequence-Specific Binding by Thomas A. Steitz. Buy a discounted Paperback of Structural Studies of Protein- ... Booktopia has Structural Studies of Protein-Nucleic Acid Interaction, ... Sequence-specific DNA-binding proteins. Sequence-independent DNA-binding proteins. Sequence-specific RNA-binding proteins. ... Structural Studies of Protein-Nucleic Acid Interaction. The Sources of Sequence-Specific Binding. By: Thomas A. Steitz. ...
Ribosomal protein; RNA-binding; KW rRNA-binding. SQ SEQUENCE 141 AA; UNKNOWN MW; UNKNOWN CRC64; MSSEYRTGRE GEEFTYRGYT ... Protein S19 forms a complex with S13 that binds strongly CC to the 16S ribosomal RNA (By similarity). CC -!- SIMILARITY: ... 2, Last sequence update) DT 00-JAN-0000 (Rel. 3, Last annotation update) DE RecName: Full=30S ribosomal protein S19P; (HALBP_1. ... DR GO; GO:0019843; F:rRNA binding; IEA:UniProtKB-KW. DR GO; GO:0003735; F:structural constituent of ribosome; IEA:InterPro. DR ...
  • FMRP controls the translation of target mRNAs in part by promoting their dynamic transport in neuronal RNA granules. (biologists.org)
  • This study opens new avenues to further elucidate the molecular mechanisms controlling FMRP trafficking with its associated mRNAs in and out of RNA granules. (biologists.org)
  • In neurons, FMRP may also act as a translational repressor by trapping mRNAs into neuronal RNA granules which are then transported out of the soma in a repressed state until they reach their destination in the neurites ( Bassell and Warren, 2008 ). (biologists.org)
  • The RGG RNA binding motif of dFMRP is dispensable for dFMRP granules formation since its deletion does not prevent formation of those granules. (biologists.org)
  • Similarly, deletion of a large part of the KH RNA binding motif of dFMRP had no effect on formation of dFMRP-granules, but diminished the shuttling activity of dFMRP. (biologists.org)
  • These RNA granules are reminiscent of neuronal granules, of stress granules, as well as of the recently described in vitro -assembled granules. (biologists.org)
  • Polypyrimidine tract binding protein inhibits IgM pre-mRNA splicing by diverting U2 snRNA base-pairing away from the branch point. (umassmed.edu)
  • Zheng X, Cho S, Moon H, Loh TJ, Oh HK, Green MR, Shen H. Polypyrimidine tract binding protein inhibits IgM pre-mRNA splicing by diverting U2 snRNA base-pairing away from the branch point. (umassmed.edu)
  • It is not known how DExD/H-box proteins manipulate structured RNA, what determines target specificity and what molecular events follow their action. (utexas.edu)
  • Our results thus suggest that the mechanisms controlling formation of RNA granules and those promoting their dynamics are uncoupled. (biologists.org)
  • Via its control of mRNA expression, the formation of RNA granules is critical for an adequate cellular response to external stimuli. (biologists.org)
  • To assess the influence of RNA sequence2.urule;structure on the interaction RNAs with the iron-responsive element binding protein (IRE-BP), twenty eight altered RNAs were tested as competitors for an RNA corresponding to the ferritin H chain IRE. (uthscsa.edu)
  • It is inferred that the IRE-BP forms multiple contacts with its cognate RNA, and that these contacts, acting in concert, provide the basis for the high affinity of this interaction. (uthscsa.edu)
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