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  • loci
  • Here, we performed a multi-disciplinary study of four highly conserved and brain-expressed transcripts selected from a list of mouse long intergenic noncoding RNA (lncRNA) loci that generally show pronounced evolutionary constraint within their putative promoter regions and across exon-intron boundaries. (biomedcentral.com)
  • genome
  • Small RNAs as guardians of the genome. (nih.gov)
  • It consists of a non-coding 222nt sRNA called RatA (RNA anti-toxin A) and a protein toxin named TxpA (Toxic protein A). RatA was discovered in intergenic regions of the B. subtilis genome, in a 728-nucleotide region between genes yqdB (later renamed TxpA) and yqbM. (wikipedia.org)
  • The combined length of repetitive sequences was 26.5 Mb, which accounted for 6.87% of the genome, indicating that the compactness of T. flavidus genome was approximative with that of T. rubripes genome.A total of 1,253 non-coding RNA genes and 30,285 protein-encoding genes were assigned to the genome.This draft genome provides a valuable resource for understanding and improving both fundamental and applied research with pufferfish in the future. (nih.gov)
  • The turnip crinkle virus (TCV) core promoter hairpin (Pr) is an RNA element located in the 3' UTR of the viral genome that is required for minus strand RNA synthesis. (wikipedia.org)
  • In order to insert itself into the genome, retrotransposon encoded protein (R2) protein makes a specific nick in one of the DNA strands at the insertion site and uses the 3′ hydroxyl group exposed by this nick to prime the reverse transcription process termed target primed reverse transcription (TPRT), where the RNA genome is transcribed into DNA. (wikipedia.org)
  • The R2 element 3' UTR RNA is a cis-acting element identified in R2 retrotransposons which is involved in priming the reverse transcription process (an essential part of retrotransposon insertion into the host genome). (wikipedia.org)
  • Flaviviruses have a (+) sense RNA genome and replicate in the cytoplasm of the host cells. (wikipedia.org)
  • regulatory
  • We want to define a dynamic RNA regulatory network for germline development by determining structures of 3'UTRs in vivo and how they change during development. (albany.edu)
  • Transposable Elements and DNA Methylation Create in Embryonic Stem Cells Human-Specific Regulatory Sequences Associated with Distal Enhancers and Noncoding RNAs. (nih.gov)
  • It is a dual-function RNA which acts both as a protein-coding RNA and as a regulatory sRNA. (wikipedia.org)
  • The Atlas of UTR Regulatory Activity (AURA), now at its second version, is a manually curated and comprehensive catalog of human 5' and 3' untranslated sequences (UTR) and UTR regulatory annotations. (wikipedia.org)
  • This, along with its presence in the majority of modern phyla, indicates that RNA editing is an essential regulatory gene for metazoan organisms. (wikipedia.org)
  • nucleotide
  • These two activities of DsrA can be separated by mutation: the first of three stem-loops of the 85 nucleotide RNA is necessary for RpoS translation but not for anti-H-NS action, while the second stem-loop is essential for antisilencing and less critical for RpoS translation. (wikipedia.org)
  • Xist RNA
  • The Xist RNA A-repeat comprises a novel AUCG tetraloop fold and a platform for multimerization. (biomedsearch.com)
  • While it is established that the 5' region of Xist RNA, comprising the A-repeats and holding 7.5-8.5 copies of a conserved 26-mer sequence, is essential for Xist-mediated silencing, high-resolution structural information for the A-repeats is not available. (biomedsearch.com)
  • XIST RNA paints and induces silencing of one X chromosome in mammalian female cells, providing a powerful model to investigate long-range chromosomal regulation. (umassmed.edu)
  • This chapter focuses on events downstream from the spread of XIST RNA across the interphase chromosome, to consider how this large noncoding RNA interacts with and silences a whole chromosome. (umassmed.edu)
  • For example, evidence indicates that XIST RNA acts at the architectural level of the whole chromosome to induce formation of a silent core enriched for nongenic and repetitive (Cot-1) DNA, which corresponds to the DAPI-dense Barr body. (umassmed.edu)
  • Regulation
  • SR1 RNA is involved in the regulation of arginine catabolism. (wikipedia.org)
  • The sequence of the first stem-loop of DsrA is complementary with the upstream leader portion of RpoS messenger RNA, suggesting that pairing of DsrA with the RpoS message might be important for translational regulation. (wikipedia.org)
  • gene
  • The gene underlying the disorder, fragile X mental retardation 1 (FMR1), is silenced in most cases by a CGG-repeat expansion mutation in the 5' untranslated region (UTR). (nih.gov)
  • The RyhB gene name is an acronym composed of R for RNA, y for unknown function (after the protein naming convention), with the h representing the ten-minute-interval section of the E. coli map the gene is found in. (wikipedia.org)
  • Early research in the 1990s looked into the specifics of vault RNA and focused around the conservation of the gene in animals. (wikipedia.org)
  • Transcription of the GcvB RNA is activated by the adjacent GcvA gene and repressed by the GcvR gene. (wikipedia.org)
  • Through its intuitive web interface, it furthermore provides full access to a wealth of information that integrates RNA sequence and structure data, variation sites, gene synteny, gene and protein expression and gene functional descriptions from scientific literature and specialized databases. (wikipedia.org)
  • Double-stranded RNA-specific adenosine deaminase is an enzyme that in humans is encoded by the ADAR gene (which stands for adenosine deaminase acting on RNA). (wikipedia.org)
  • Adenosine Deaminase Acting on RNA (ADAR) and its gene were first discovered accidentally in 1987 as a result of research by Brenda Bass and Harold Weintraub. (wikipedia.org)
  • This likely occurred in the lineage which leads to the crown Metazoa when a duplicate ADAT gene was coupled to a gene encoding at least one double stranded RNA binding. (wikipedia.org)
  • structures
  • We also show that RNA secondary structures can be compared very rapidly by a simple string Edit-Distance algorithm with a minimal loss of accuracy.These datasets allowed for comparison of the algorithm with other methods.In these tests, RNAspa performed better than four other programs. (nih.gov)
  • We also show that RNA secondary structures can be compared very rapidly by a simple string Edit-Distance algorithm with a minimal loss of accuracy. (nih.gov)
  • Secondary structures for 5' regions of R2 retrotransposon RNAs reveal a novel conserved pseudoknot and regions that evolve under different constraints. (wikipedia.org)
  • Cellular RNA cap structures are formed via the action of an RNA triphosphatase, with guanylyltransferase, N7-methyltransferase and 2′-O methyltransferase. (wikipedia.org)
  • The N-terminal domain of the non-structural protein 5 (NS5) has both the N7-methyltransferase and guanylyltransferase activities necessary for forming mature RNA cap structures. (wikipedia.org)
  • Dicer
  • Through recent discoveries, it has been shown that the vault non-coding RNAs produce small vault RNAs through a DICER mechanism. (wikipedia.org)
  • molecule
  • A single example of Type III toxin-antitoxin system has been described whereby a protein toxin is bound directly by an RNA molecule. (wikipedia.org)
  • vivo
  • First, RNA synthesized in vitro competes with the hybridization of [(32)P]rRNA synthesized in vivo to the heavy strand of B. subtilis DNA. (jove.com)
  • Second, unlabeled rRNA synthesized in vivo competes with the hybridization of [(3)H]RNA synthesized in vitro to denatured DNA or heavy-strand DNA, but not to light-strand DNA. (jove.com)
  • antitoxin
  • TA systems controlled by interaction between toxin protein and antitoxin RNA have been identified in S. aureus in silico , but not yet experimentally proven. (mdpi.com)
  • Toxin-antitoxin system Hok/sok system RdlD RNA Silvaggi JM, Perkins JB, Losick R (October 2005). (wikipedia.org)
  • intergenic
  • Ongoing studies are also addressing the role of long, intergenic non-coding RNAs in regulating stem cell function. (stanford.edu)
  • Chemical
  • Dependent on the chemical nature of the antitoxins (protein or RNA) and how they control the activity of the toxin, TA systems are currently divided into six different types. (mdpi.com)
  • Isoenergetic penta- and hexanucleotide microarray probing and chemical mapping provide a secondary structure model for an RNA element orchestrating R2 retrotransposon protein function. (wikipedia.org)
  • Humans
  • A) Patterns of the full-length sequence conservation of 826 human ESC-specific NANOG-binding sites (left panel) and 130 genomic loci encoding 33 nt LTR7 RNA (right panel) in genomes of five Modern Humans and three Neanderthals. (nih.gov)
  • So far vault RNAs have been isolated from humans, rodents and bullfrogs. (wikipedia.org)
  • genomic
  • Here, we review the conserved roles played by small RNAs in the adaptation of eukaryotes to coexist with their genomic colonists. (nih.gov)
  • The genomic RNA is modified at the 5′ end of positive-strand genomic RNA with a cap-1 structure (me7-GpppA-me2). (wikipedia.org)
  • Flavivirus genomic RNA replication occurs on rough endoplasmic reticulum membranes in membranous compartments. (wikipedia.org)
  • Sequences
  • A) Generation of scan RNAs (scnRNAs) from the eliminated (green) and noneliminated (orange) germline sequences. (nih.gov)
  • indicates
  • This positioning of the RNA indicates that they could interact with both the interior and exterior of the vault particle. (wikipedia.org)
  • region
  • A 3' untranslated region variant in FMR1 eliminates neuronal activity-dependent translation of FMRP by disrupting binding of the RNA-binding protei. (nih.gov)
  • The vimentin 3' UTR protein-binding region is an RNA element that contains a Y shaped structure which has been shown to have protein binding activity. (wikipedia.org)
  • An RNA fragment found in the R2 3' untranslated region (3'UTR), has been shown to interact with one copy of R2 protein during TPRT. (wikipedia.org)
  • dsRNA
  • Adenosine deaminases acting on RNA (ADAR) are enzymes responsible for binding to double stranded RNA (dsRNA) and converting adenosine (A) to inosine (I) by deamination. (wikipedia.org)
  • It was also shown that this protein is specific for double stranded RNA, or dsRNA, and does not require ATP. (wikipedia.org)
  • found
  • Most editing site are found in noncoding regions of RNA such as untranslated regions (UTRs), Alu elements and long interspersed nuclear element (LINEs). (wikipedia.org)
  • secondary
  • Sequence comparisons show evidence for compensatory mutations within the helical regions indicating the secondary structure of the RNA is of biological importance. (wikipedia.org)
  • occurs
  • This processing occurs via a self-cleaving ribozyme that forms at the 5' junction of the R2 RNA. (wikipedia.org)
  • To date, conservation of structure has only been described in five moth species: Bombyx mori (R2Bm), Samia cynthia (R2Sc), Coscinocera hercules (R2Ch), Callosamia promethea (R2Cpr), Saturnia pyri (R2Spy) Within this 5' protein binding site an RNA pseudoknot structure occurs. (wikipedia.org)
  • retrotransposons
  • One research project relates to intron dispersal under cell stress, and to the structure and function of a catalytic RNA that is related to mammalian introns and retrotransposons. (albany.edu)
  • interactions
  • Projects in our lab examine the interactions and mechanisms by which RNA viruses such as hepatitis C virus exploit host microRNAs and RNA granules to promote infection. (albany.edu)