• genes
  • 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)
  • Most known regulatory RNAs are encoded by independent genes (sRNAs), while 15 transcripts are partly generated from the antisense strands of coding sequences (aRNAs) and may affect translation or stability of overlapping mRNAs. (jbsdonline.com)
  • Most human genes transcribed by RNA Pol II (polymerase II) contain short exons separated by long tracts of non-coding intronic sequences. (ox.ac.uk)
  • Cross-tissue comparison revealed that the transcriptional profiles of pseudogenes and their parent genes showed mostly positive correlations, suggesting that pseudogene transcription could have a positive effect on the expression of their parent genes, perhaps by functioning as competing endogenous RNAs (ceRNAs), as previously suggested and demonstrated with the PTEN pseudogene, PTENP1. (nih.gov)
  • The B comes from the fact that this was one of two RNA genes identified in this interval. (wikipedia.org)
  • The gcvB RNA gene encodes a small non-coding RNA involved in the regulation of a number of amino acid transport systems as well as amino acid biosynthetic genes. (wikipedia.org)
  • GcvB RNA also is involved in regulating a variety of genes involved in amino acid biosynthesis such as ilvC, gdhA, thrL and serA. (wikipedia.org)
  • The center contains twelve genes, seven of which code for proteins, five for untranslated RNAs, of which only two are known to play an active role in the X inactivation process, Xist and Tsix. (wikipedia.org)
  • These researchers were using antisense RNA inhibition to determine which genes play a key role in the development of Xenopus leavis embryos. (wikipedia.org)
  • The R2 RNA element is a non-long terminal repeat (non-LTR) retrotransposable element that inserts at a specific site in the 28S ribosomal RNA (rRNA) genes of most insect genomes. (wikipedia.org)
  • Proteins
  • Although the identity and properties of proteins and noncoding RNAs that execute dosage compensation are known in detail, much less is known about the cis -acting factors that must reside on the X chromosome to recruit the dosage compensation machinery. (genetics.org)
  • The vault complex comprises the major vault protein (MVP), two minor vault proteins (VPARP and TEP1), and a variety of small untranslated RNA molecules. (wikipedia.org)
  • While vault proteins appear to be present in a variety of organisms, vaults isolated from higher eukaryotes contain a small portion, about 5%, of small untranslated RNAs called vault RNAs, or vtRNAs. (wikipedia.org)
  • It includes basic annotation, phylogenetic conservation, binding sites for RNA-binding proteins and miRNA, cis-elements, RNA methylation and editing data, and more, for human and mouse. (wikipedia.org)
  • The IRE is a stem-loop structure within the untranslated regions of mRNAs that encode proteins involved in cellular iron metabolism. (wikipedia.org)
  • genome
  • In any case two methods for the genome-wide mapping of RNA polymerase binding sites complement each other. (jbsdonline.com)
  • 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)
  • 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)
  • 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)
  • antisense
  • The highest percentage of promoters followed by putative ORFs (56%) has been found in group I regions, while the smallest one in group A (26%), assuming that most RNAs potentially produced in antisense direction within coding regions may function as untranslated RNAs. (jbsdonline.com)
  • moreover, it showed that many human pseudogenes produced small RNAs (sRNAs) and some pseudogene-derived sRNAs, especially those from antisense strands, exhibited evidence of interfering with gene expression. (nih.gov)
  • There is evidence that DsrA RNA can self-assemble into nanostructures through antisense interactions of three self-complementary regions. (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)
  • mRNAs
  • Physico-chemical properties of predicted RNA-products were compared with those of known sRNAs and mRNAs of comparable size. (jbsdonline.com)
  • gene
  • The MicX RNA gene overlaps with VCA0943 - a gene coding for a maltose transporter permease - but the ribonuclease RNAase E processes the MicX transcript to create an active and stable form containing only the VCA0943 3' UTR. (wikipedia.org)
  • 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)
  • 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)
  • transcript
  • X-chromosome inactivation (XCI) in female mammals depends on the noncoding RNA X inactivation specific transcript (Xist). (biomedsearch.com)
  • Initially, Affymetrix microarrays were used to detect transcription in this region, Northern blot experiments and mutation analysis were then employed to characterise the RNA transcript. (wikipedia.org)
  • regions
  • 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)
  • Sequence comparisons show evidence for compensatory mutations within the helical regions indicating the secondary structure of the RNA is of biological importance. (wikipedia.org)
  • Secondary structures for 5' regions of R2 retrotransposon RNAs reveal a novel conserved pseudoknot and regions that evolve under different constraints. (wikipedia.org)
  • mechanism
  • Through recent discoveries, it has been shown that the vault non-coding RNAs produce small vault RNAs through a DICER mechanism. (wikipedia.org)
  • microRNAs
  • 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)
  • inactivation
  • Expression of repeat RNAs may contribute to chromosome remodeling, and evidence suggests that other types of repeat elements may be involved in escape from X inactivation. (umassmed.edu)
  • expression
  • D) Expression levels of RNA expression driven by M3_2 together with regulating TFs at cellular resolution, as shown in the key. (nih.gov)
  • single stranded
  • ADAR2 and ADAR3 have an arginine rich single stranded RNA (ssRNA) binding domain. (wikipedia.org)
  • Flaviviruses share several common aspects: common size (40-65 nm), symmetry (enveloped, icosahedral nucleocapsid), nucleic acid (positive-sense, single-stranded RNA around 10,000-11,000 bases), and appearance in the electron microscope. (wikipedia.org)
  • mammalian
  • 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)
  • structures
  • 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)
  • genomic
  • 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)
  • 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)
  • indicates
  • This positioning of the RNA indicates that they could interact with both the interior and exterior of the vault particle. (wikipedia.org)
  • sRNAs
  • Although these values fall in the range of sizes of known sRNAs (34-465 nt), many predicted RNAs are longer than sRNAs. (jbsdonline.com)
  • RyhB
  • Northern blot with RyhB probe on total RNA was performed at an OD600 of 0.5 along with β-galactosidase assays. (nih.gov)
  • region
  • 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)
  • function
  • Ongoing studies are also addressing the role of long, intergenic non-coding RNAs in regulating stem cell function. (stanford.edu)
  • Post Doctoral Associate: the anti-apoptotic function of virally expressed untranslated RNA. (ucl.ac.uk)
  • 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)
  • computational
  • To explore these issues systematically, we first developed a computational pipeline to identify transcribed pseudogenes from RNA-Seq data. (nih.gov)