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DNA Transposable ElementsResponse ElementsEnhancer Elements, GeneticPromoter Regions, GeneticTranscription, GeneticBase SequenceRegulatory Sequences, Nucleic AcidTrace ElementsFinite Element AnalysisMolecular Sequence DataElementsAlu ElementsShort Interspersed Nucleotide ElementsTranscription FactorsDNA-Binding ProteinsLong Interspersed Nucleotide ElementsGene Expression RegulationRegulatory Elements, TranscriptionalBinding SitesRepetitive Sequences, Nucleic AcidAmino Acid SequenceDNASequence Homology, Nucleic AcidRNA, MessengerPlasmidsCell LineMutationCloning, MolecularTransfectionGenes, ReporterRetroelementsSequence Analysis, DNARestriction MappingConserved SequenceNucleic Acid ConformationNuclear ProteinsSequence DeletionChloramphenicol O-AcetyltransferaseIntronsTranscriptional ActivationSequence AlignmentProtein BindingGenes, RegulatorDNA PrimersHeLa CellsConsensus SequencePhylogenyTransposasesDrosophila melanogasterChromosome MappingModels, GeneticInsulator ElementsInterspersed Repetitive SequencesRecombinant Fusion ProteinsPolymerase Chain ReactionTime FactorsMutagenesis, Site-DirectedLuciferasesOligodeoxyribonucleotides3' Untranslated RegionsRepressor ProteinsExonsCells, CulturedDNA FootprintingTrans-ActivatorsDeoxyribonuclease ICell NucleusGenesSilencer Elements, TranscriptionalRegulatory Sequences, Ribonucleic AcidTerminal Repeat SequencesSequence Homology, Amino Acid5' Untranslated RegionsMutagenesis, InsertionalModels, BiologicalSp1 Transcription FactorSpecies SpecificityCyclic AMP Response Element-Binding ProteinEscherichia coliElectrophoretic Mobility Shift AssayRNAE-Box ElementsTumor Cells, CulturedBlotting, SouthernGene Expression Regulation, EnzymologicDNA, BacterialShort Bowel SyndromeDrosophilaProtein Structure, TertiarySaccharomyces cerevisiaeGene ExpressionMultigene FamilyRNA-Binding ProteinsModels, MolecularRecombination, GeneticProtein BiosynthesisSignal TransductionMutagenesisRecombinant Proteins5' Flanking Region
SINEsTransposableNUCLEOTIDE ELEMENTSRepeatsNuclearRepetitive sequencesRetrotransposonsEukaryotic genomesGenomesRETROELEMENTSHumansProteinsIntergenicIntronsInsertionsLongCopiesGeneTransposonsEndogenousClassesRNAsPromoterAbundantHumanMakeGenetic elementsSpoken wordComplexHighlyStoriesInsertionMolecularOrganizationSeveral shortIdentificationSpacePiecesClassSpecies
SINEs9
  • Short interspersed nuclear elements (SINEs) are non-autonomous, non-coding transposable elements (TEs) that are about 100 to 700 base pairs in length. (wikipedia.org)
  • However, eukaryotes have been able to integrate short-interspersed nuclear elements into different signaling, metabolic and regulatory pathways and SINEs have become a great source of genetic variability. (wikipedia.org)
  • Short-interspersed nuclear elements which only possess a head and tail are called simple SINEs whereas short-interspersed nuclear elements which also possess a body or are a combination of two or more SINEs are complex SINEs. (wikipedia.org)
  • This generates a vast repertoire of transcripts that includes protein-coding messenger RNAs, long non-coding RNAs (lncRNAs) and repetitive sequences, such as SINEs (short interspersed nuclear elements). (nature.com)
  • Both LINEs and SINEs elements, despite the differences in structure and transposition mechanisms ( [44] ), are ubiquitous components of eukaryotic genomes, playing a major role in their evolution. (sisef.it)
  • There are 250000 copies of LINE elements in Lilium ( [21] ) and SINEs are represented, for example, by 50000 copies in tobacco ( [46] ). (sisef.it)
  • Okada N. SINEs: short interspersed repeated elements of the eukaryotic genome. (medecinesciences.org)
  • Mammalian DNA, including the human genome, contains about 1 million SINEs (short interspersed nuclear elements), noncoding mobile genetic elements that make up about 10% of the total genome. (medicalxpress.com)
  • SINEs are a class of non-autonomous mobile elements and are essentially homoplasy-free characters with known ancestral states, making them useful genetic markers for phylogenetic studies. (biomedcentral.com)
Transposable9
  • Most of these sequences qualify as junk but they are littered with defective transposable elements that are already included in the calculation of junk DNA. (blogspot.com)
  • Here we present the Rice TE database (RiTE-db) - a genus-wide collection of transposable elements and repeated sequences across 11 diploid species of the genus Oryza and the closely-related out-group Leersia perrieri . (biomedcentral.com)
  • In addition to the annotation of gene space, a detailed annotation of repeated sequences and transposable elements (TEs) ( e.g. presence/absence, types, and location) is critical for understanding the biology of a genome, as well as an important tool for the improvement of high-quality genome assemblies. (biomedcentral.com)
  • The use of repeat libraries of one species to detect repeats from a related species (that diverged e.g. 10 million years ago) is highly problematic as it is known that intergenic space is rapidly evolving for the high turnover rates of transposable elements and repetitive sequence. (biomedcentral.com)
  • Unfortunately, high-copy number repeats and transposable elements are not well represented in most genome assemblies. (biomedcentral.com)
  • Illumina): highly repetitive sequences and transposable elements pose significant problems to assembly algorithms. (biomedcentral.com)
  • Transposable elements (TEs) are ancient (retro)-virus insertions inside a host genome and are peculiar mobile genetic elements accounting for a large proportion of repetitive DNA regions ( [29] ). (sisef.it)
  • We find that most sequence elements, including most classes of transposable elements, acquire methylation at similar rates overall. (biomedcentral.com)
  • The Dnmt3a and Dnmt3L genes are critical mediators of cytosine methylation during gametogenesis, with major actions noted at transposable elements and imprinted loci. (elsevierpure.com)
NUCLEOTIDE ELEMENTS1
Repeats5
  • these simple repeats are sites where two (or more) short-interspersed nuclear elements can combine to form a dimeric SINE. (wikipedia.org)
  • For example, one copy of a specific short tandem repeat (STR) region might have 10 repeats, while the other copy might have 11 repeats. (ojp.gov)
  • This is the first report of a repeat dataset that spans the majority of repeat variability within an entire genus, and one that includes complete elements as well as unassembled repeats. (biomedcentral.com)
  • This system consists of CRISPR (clustered regularly interspersed short palindromic repeats) and CRISPR-associated (Cas) proteins. (benthamscience.com)
  • This track was created by using Arian Smit's RepeatMasker program, which screens DNA sequences for interspersed repeats and low complexity DNA sequences. (noncode.org)
Nuclear5
  • In essence, short interspersed nuclear elements are genetic parasites which have evolved very early in the history of eukaryotes to utilize protein machinery within the organism as well as to co-opt the machinery from similarly parasitic genomic elements. (wikipedia.org)
  • The different lineages, mutations, and activities among eukaryotes make short-interspersed nuclear elements a useful tool in phylogenetic analysis. (wikipedia.org)
  • Short-interspersed nuclear elements are transcribed by RNA polymerase III which is known to transcribe ribosomal RNA and tRNA, two types of RNA vital to ribosomal assembly and mRNA translation. (wikipedia.org)
  • In other words, short-interspersed nuclear elements have their key promoter elements within the transcribed region itself. (wikipedia.org)
  • Long interspersed nuclear element-1 (L1) retrotransposons are a source of divergent genetic information in hominoid genomes, but their importance in physiological functions and their contribution to human brain evolution are largely unknown. (lu.se)
Repetitive sequences1
Retrotransposons6
  • They are a class of retrotransposons, DNA elements that amplify themselves throughout eukaryotic genomes, often through RNA intermediates. (wikipedia.org)
  • Two retrotransposons, belonging to the two major classes of LTR and non-LTR elements, were characterized trough a SCAR (Sequence Characterized Amplified Region) strategy. (sisef.it)
  • The cloning and sequencing of amplification products and a Cleaved Amplified Polymorphisms (CAPs) approach on the identified retrotransposons, showed a high level of diversity among the multiple copies of both elements. (sisef.it)
  • Non-LTR retrotransposons can be divided in several subclasses, such as LINE (Long INterspersed Elements) and SINE (Short INterspersed Elements - [44] ). (sisef.it)
  • The observed differences in genome size in plants are accompanied by variations in the content of LTR retrotransposons, demonstrating that such elements might be important players in the evolution of plant genomes, along with polyploidy ( [11] ). (sisef.it)
  • To investigate the expression of long interspersed element (LINE) 1, human endogenous retrovirus (HERV) K10, and short interspersed element-VNTR-Alu element (SVA) retrotransposons in ejaculated human spermatozoa by means of reverse-transcription (RT) polymerase chain reaction (PCR) analysis as well as the potential incorporation of cloned human and mouse active retroelements in human sperm cell genome. (nih.gov)
Eukaryotic genomes2
  • It is therefore clear that retrotransposable elements build large parts of eukaryotic genomes ( [40] ). (sisef.it)
  • Wide distribution of short interspersed elements among eukaryotic genomes. (medecinesciences.org)
Genomes1
  • The simplicity of these elements make them remarkably successful at persisting and amplifying (through retrotransposition) within the genomes of eukaryotes. (wikipedia.org)
RETROELEMENTS1
  • Notably, the L1 element can retrotranspose itself as well as other retroelements, such as Alu and SVA (SINE-VNTR-Alu: short interspersed element-variable number tandem repeat-Alu). (researchsquare.com)
Humans2
  • Exaptation of an ancient Alu short interspersed element provides a highly conserved vitamin D-mediated innate immune response in humans and primates. (oregonstate.edu)
  • SVA elements are~2-kb hominid-specific noncoding RNAs that have resulted in single-gene disease in humans through insertional mutagenesis or aberrant mRNA splicing. (elsevierpure.com)
Proteins1
  • Furthermore, the shape and density of certain areas of a chromosome can affect the shape and density of neighboring (or even distant regions) on the chromosome through interaction facilitated by different proteins and elements. (wikipedia.org)
Intergenic1
  • However, these intergenic regions carry important elements that regulate gene activity, for instance, the promoter where transcription starts, and enhancers and silencers that fine-tune gene expression. (jove.com)
Introns1
Insertions2
  • In total, KoVariome includes 12.7M single-nucleotide variants (SNVs), 1.7M short insertions and deletions (indels), 4K structural variations (SVs), and 3.6K copy number variations (CNVs). (nature.com)
  • Nikaido M, Rooney AP, Okada N. Phylogenetic relationships among cetartiodactyls based on insertions of short and long interspersed elements: hippopotamuses are the closest extant relatives of whales. (medecinesciences.org)
Long3
  • non-LTR and LTR elements characterized, respectively, by the absence or presence of long repeated regions flanking the ORFs core. (sisef.it)
  • The retroelement long interspersed element-1 ( LINE-1 or L1) comprises about 17% of the human genome. (researchsquare.com)
  • The long interspersed element 1 (LINE-1 or L1) ORF2 protein is the genomic source for RT activity required for mobilization of its own RNA in cis and other RNAs, such as SINE/variable-number tandem-repeat (VNTR)/Alu (SVA) elements, in trans. (elsevierpure.com)
Copies2
  • The analysis demonstrated the presence of multiple copies of retrotransposable elements inside the genome of beech, in accordance with the viral quasi-species theory of retrotransposon evolution. (sisef.it)
  • the gypsy LTR element is present in 20000 copies in maize. (sisef.it)
Gene2
  • These short RNAs participate in a diverse array of cellular processes including gene regulation, chromatin dynamics and genome defense. (biomedcentral.com)
  • The study highlighted several mechanisms underlying species diversification, including selection acting on existing standing variation, high rates of gene duplication, novel microRNAs and rapid sequence divergence in otherwise conserved non-coding elements. (biomedcentral.com)
Transposons1
  • Both deletions and inversions show a significant overlap with SINE elements, while inversions additionally show a limited, but significant association with DNA transposons. (biomedcentral.com)
Endogenous1
  • the 5' head is indicative of which endogenous element that SINE was derived from and was able to parasitically utilize its transcriptional machinery. (wikipedia.org)
Classes3
  • As part of the genome sequencing initiative for the tammar, we have explored the evolution of each of the major classes of mammalian small RNAs in an Australian marsupial for the first time, including the first genome-scale analysis of the newest class of small RNAs, centromere repeat associated short interacting RNAs (crasiRNAs). (biomedcentral.com)
  • Using next generation sequencing, we have characterized the major classes of small RNAs, micro (mi) RNAs, piwi interacting (pi) RNAs, and the centromere repeat associated short interacting (crasi) RNAs in the tammar. (biomedcentral.com)
  • There are two classes of interspersed repetitive elements. (edu.au)
RNAs1
  • PU.1 expression is modulated by the balance of functional sense and antisense RNAs regulated by a shared cis-regulatory element. (nature.com)
Promoter1
  • These transcripts are almost evenly divided between those arising from enhancer-associated (elncRNA) or promoter-associated (plncRNA) elements. (biomedcentral.com)
Abundant1
  • For example, the 5' of the Alu sine is derived from 7SL RNA, a sequence transcribed by RNA Polymerase III which codes for the RNA element of SRP, an abundant ribonucleoprotein. (wikipedia.org)
Human1
Make1
  • It seems it's just as ambitious to tell a story succinctly, to have a short amount of pages make up one's entire enterprise. (bigother.com)
Genetic elements1
Spoken word1
  • Released on the 1969 album, Karma , which was produced by Bob Thiele (he worked on Coltrane's albums, too), "The Creator Has a Master Plan" has elements of spoken word, psychedelia, minimalism, and even balladeering. (kqed.org)
Complex1
  • Lectures will cover all aspects of the toolkit from basic installation through advanced topics and will be interspersed with examples that build a progressively more complex application, extensib le to real space and medical use. (infn.it)
Highly1
  • 7. Ross BC, Raios K, Jackson K, Dwyer B. Molecular cloning of a highly repeated DNA element from Mycobacterium tuberculosis and its use as an epidemiological tool. (cdc.gov)
Stories2
  • The book in our hands is a series of short murder mystery stories, interspersed with McCallister's mathematical analysis of the murder mystery. (auntagathas.com)
  • By the late 80s/early 90s, the Minimalist realists (the Lish school) were in dominance, major publishers were putting out flash fiction anthologies [ Sudden Fiction: American Short-Short Stories (Gibbs Smith 1983), Flash Fiction: 72 Very Short Stories (Norton & Company 1992), Charles Simic was winning the Pulitzer for a prose poetry collection , etc. (bigother.com)
Insertion2
  • Retrotransposable elements are important and peculiar genetic components derived from ancient retrovirus insertion inside plants genome. (sisef.it)
  • The level of color shading in the graphical display reflects the amount of base mismatch, base deletion, and base insertion associated with a repeat element. (noncode.org)
Molecular1
  • In this paper the molecular identification of retrotransposable elements in Fagus sylvatica L. is reported. (sisef.it)
Organization1
  • These elements require timely and efficient organization of measures, in order for productive process of growth and development with impact on mortality, re-hospitalization, vulnerable situations, and quality of life. (bvsalud.org)
Several short2
  • Interspersed throughout the proceedings there will be several short video clips and musical interludes performed by an international orchestra conducted by world renowned conductor Vladimir Spivakov accompanied by an international choir. (yadvashem.org)
  • It consists mainly of rhyming verse and haiku, accompanied by several short prose pieces. (sabotagereviews.com)
Identification1
  • The identification of retrotransposable elements in forest trees represents an important step toward the understanding of mechanisms of genome evolution. (sisef.it)
Space1
  • Cabin of rainforest style presents a Movie Set, a short-journey-like space that belongs to explorers. (archilovers.com)
Pieces1
  • I don't think there's much battle left to be fought over the value of shorter pieces. (bigother.com)
Class1
  • Fig. 1 - Schematic representation of the general structure of class I RNA mediated LTR TE (A), class I RNA mediated non-LTR elements (B) and class II DNA mediated elements (C) in their autonomous and non autonomous configurations. (sisef.it)
Species1
  • Retrotransposable elements are well characterized in model or crop species like Arabidopsis thaliana and Oryza sativa , but are poorly known in forest tree species. (sisef.it)