An order of the class Insecta. Wings, when present, number two and distinguish Diptera from other so-called flies, while the halteres, or reduced hindwings, separate Diptera from other insects with one pair of wings. The order includes the families Calliphoridae, Oestridae, Phoridae, SARCOPHAGIDAE, Scatophagidae, Sciaridae, SIMULIIDAE, Tabanidae, Therevidae, Trypetidae, CERATOPOGONIDAE; CHIRONOMIDAE; CULICIDAE; DROSOPHILIDAE; GLOSSINIDAE; MUSCIDAE; TEPHRITIDAE; and PSYCHODIDAE. The larval form of Diptera species are called maggots (see LARVA).
The invasion of living tissues of man and other mammals by dipterous larvae.
Infection with larvae of the blow fly Cochliomyia hominivorax (Callitroga americanum), a common cause of disease in livestock in the southern and southwestern U.S.A.
Domesticated farm animals raised for home use or profit but excluding POULTRY. Typically livestock includes CATTLE; SHEEP; HORSES; SWINE; GOATS; and others.
The relationships of groups of organisms as reflected by their genetic makeup.
A family of the order DIPTERA that comprises the mosquitoes. The larval stages are aquatic, and the adults can be recognized by the characteristic WINGS, ANIMAL venation, the scales along the wing veins, and the long proboscis. Many species are of particular medical importance.
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.
The profession of writing. Also the identity of the writer as the creator of a literary production.
Collections of facts, assumptions, beliefs, and heuristics that are used in combination with databases to achieve desired results, such as a diagnosis, an interpretation, or a solution to a problem (From McGraw Hill Dictionary of Scientific and Technical Terms, 6th ed).
Sequences of DNA or RNA that occur in multiple copies. There are several types: INTERSPERSED REPETITIVE SEQUENCES are copies of transposable elements (DNA TRANSPOSABLE ELEMENTS or RETROELEMENTS) dispersed throughout the genome. TERMINAL REPEAT SEQUENCES flank both ends of another sequence, for example, the long terminal repeats (LTRs) on RETROVIRUSES. Variations may be direct repeats, those occurring in the same direction, or inverted repeats, those opposite to each other in direction. TANDEM REPEAT SEQUENCES are copies which lie adjacent to each other, direct or inverted (INVERTED REPEAT SEQUENCES).
The guidelines and policy statements set forth by the editor(s) or editorial board of a publication.
Intentional falsification of scientific data by presentation of fraudulent or incomplete or uncorroborated findings as scientific fact.
"The business or profession of the commercial production and issuance of literature" (Webster's 3d). It includes the publisher, publication processes, editing and editors. Production may be by conventional printing methods or by electronic publishing.
DNA analogs containing neutral amide backbone linkages composed of aminoethyl glycine units instead of the usual phosphodiester linkage of deoxyribose groups. Peptide nucleic acids have high biological stability and higher affinity for complementary DNA or RNA sequences than analogous DNA oligomers.
Studies beyond the bachelor's degree at an institution having graduate programs for the purpose of preparing for entrance into a specific field, and obtaining a higher degree.
The teaching staff and members of the administrative staff having academic rank in an educational institution.
Individuals enrolled in a school or formal educational program.
Educational programs for pharmacists who have a bachelor's degree or a Doctor of Pharmacy degree entering a specific field of pharmacy. They may lead to an advanced degree.
The teaching staff and members of the administrative staff having academic rank in a medical school.
Auditory and visual instructional materials.
The educational process of instructing.
Discrete segments of DNA which can excise and reintegrate to another site in the genome. Most are inactive, i.e., have not been found to exist outside the integrated state. DNA transposable elements include bacterial IS (insertion sequence) elements, Tn elements, the maize controlling elements Ac and Ds, Drosophila P, gypsy, and pogo elements, the human Tigger elements and the Tc and mariner elements which are found throughout the animal kingdom.
Enzymes that recombine DNA segments by a process which involves the formation of a synapse between two DNA helices, the cleavage of single strands from each DNA helix and the ligation of a DNA strand from one DNA helix to the other. The resulting DNA structure is called a Holliday junction which can be resolved by DNA REPLICATION or by HOLLIDAY JUNCTION RESOLVASES.
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.
A species of fruit fly much used in genetics because of the large size of its chromosomes.
The sequence of PURINES and PYRIMIDINES in nucleic acids and polynucleotides. It is also called nucleotide sequence.
A plant species of the family POACEAE. It is a tall grass grown for its EDIBLE GRAIN, corn, used as food and animal FODDER.
All of the divisions of the natural sciences dealing with the various aspects of the phenomena of life and vital processes. The concept includes anatomy and physiology, biochemistry and biophysics, and the biology of animals, plants, and microorganisms. It should be differentiated from BIOLOGY, one of its subdivisions, concerned specifically with the origin and life processes of living organisms.
A publication issued at stated, more or less regular, intervals.
A bibliographic database that includes MEDLINE as its primary subset. It is produced by the National Center for Biotechnology Information (NCBI), part of the NATIONAL LIBRARY OF MEDICINE. PubMed, which is searchable through NLM's Web site, also includes access to additional citations to selected life sciences journals not in MEDLINE, and links to other resources such as the full-text of articles at participating publishers' Web sites, NCBI's molecular biology databases, and PubMed Central.
Lists of persons or organizations, systematically arranged, usually in alphabetic or classed order, giving address, affiliations, etc., for individuals, and giving address, officers, functions, and similar data for organizations. (ALA Glossary of Library and Information Science, 1983)
The complete genetic complement contained in the DNA of a set of CHROMOSOMES in a HUMAN. The length of the human genome is about 3 billion base pairs.
"Nucleic Acids Research. 13 (12): 4401-4410. doi:10.1093/nar/13.12.4401. PMC 321795. PMID 2409535.. ... De novo repeat identification is an initial scan of sequence data that seeks to find the repetitive regions of the genome, and ... A transposable element (TE or transposon) is a DNA sequence that can change its position within a genome, sometimes creating or ... "Nucleic Acids Res. 36 (7): 2284-94. doi:10.1093/nar/gkn064. PMC 2367713. PMID 18287116.. ...
... repetitive sequences, nucleic acid MeSH G06.184.603.080.708.330 - interspersed repetitive sequences MeSH G06.184.603.080. ... 708.330.200 - dna transposable elements MeSH G06.184.603.080.708.330.200.500 - integrons MeSH G06.184.603.080.708.330.330 - ... amino acid MeSH G06.184.842.200.820 - structural homology, protein MeSH G06.184.842.550 - sequence homology, nucleic acid MeSH ... repetitive sequences, amino acid MeSH G06.184.603.060.720.030 - ankyrin repeat MeSH G06.184.603.080 - base sequence MeSH ...
Strand DJ, McDonald JF (June 1985). "Copia is transcriptionally responsive to environmental stress". Nucleic Acids Research. 13 ... "Computational Approaches and Tools Used in Identification of Dispersed Repetitive DNA Sequences". Tropical Plant Biol. 1: 85-96 ... A transposable element (TE, transposon, or jumping gene) is a DNA sequence that can change its position within a genome, ... When the transposable elements lack additional genes, they are known as insertion sequences. In humans, the most common TE is ...
Vansant, G; Reynolds, W. F (1995). "The consensus sequence of a major Alu subfamily contains a functional retinoic acid ... and provided the definitive link between transposable elements (active elements) and interspersed repetitive DNA (mutated ... Schmid, C. W (1998). "Does SINE evolution preclude Alu function?". Nucleic Acids Research. 26 (20): 4541-50. doi:10.1093/nar/ ... Häsler, Julien; Strub, Katharina (2006). "Alu elements as regulators of gene expression". Nucleic Acids Research. 34 (19): 5491 ...
Repeated sequences (also known as repetitive elements, repeating units or repeats) are patterns of nucleic acids (DNA or RNA) ... interspersed nuclear elements): Transposable elements. DNA transposons.retrotransposons.LTR-retrotransposons (HERVs).non LTR- ... "The 3D folding of metazoan genomes correlates with the association of similar repetitive elements". Nucleic Acids Research. 44 ... with over two-thirds of the sequence consisting of repetitive elements in humans. Repetitive elements found in genomes fall ...
ORF1 trimers have RNA-binding and nucleic acid chaperone activity that are necessary for retrotransposition. The second ORF of ... "Binding of the ubiquitous nuclear transcription factor YY1 to a cis regulatory sequence in the human LINE-1 transposable ... can further impact genome variation by mispairing and unequal crossing-over during meiosis due to its repetitive DNA sequences ... International Human Genome Sequencing Consortium) (February 2001). "Initial sequencing and analysis of the human genome". ...
"Identification of a conserved sequence in the non-coding regions of many human genes". Nucleic Acids Research. 17 (2): 699-722 ... Jurka, Jerzy; Walichiewicz, Jolanta; Milosavljevic, Aleksandar (October 1992). "Prototypic sequences for human repetitive DNA ... Mammalian-wide interspersed repeats (MIRs) are transposable elements in the genomes of some organisms and belong to the group ... Nucleic Acids Research. 23 (1): 98-102. doi:10.1093/nar/23.1.98. PMC 306635. PMID 7870595. Lander; et al. (2001). "Initial ...
Alternative splicing Altruism Alu family Alzheimer's disease Amber codon Ames test Amino acid Amino acid sequence Amino acids ... Norm of reaction Normal distribution Northern analysis Northern blot NPD Nu body Nuclear transfer Nuclease Nucleic acid ... element Regulator gene Relaxed mutant Renal cell cancer Renal cell carcinoma Renner complex Repeat sequences Repetitive DNA ... Translocation Transposable element Transposition Transposon Transversion Trihybrid Triplet Triplet code Triploid Trisomic ...
Molecular pathology Nucleic acid sequence Pan-genome Precision medicine Regulator gene Sequenceome Whole genome sequencing Roth ... However, this special characteristic is caused by the presence of repetitive DNA, and transposable elements (TEs). A typical ... Noncoding sequences include introns, sequences for non-coding RNAs, regulatory regions, and repetitive DNA. Noncoding sequences ... New sequencing technologies, such as massive parallel sequencing have also opened up the prospect of personal genome sequencing ...
Amino acid sequences and nucleic acid sequences do not mutate at the same rate. Due to the degenerate nature of DNA, bases can ... Many transposable elements are related to viruses, and share several proteins in common. The number of chromosomes in an ... Genome size is influenced by the amount of repetitive DNA as well as number of genes in an organism. The C-value paradox refers ... nucleic acid sequencing allowed molecular evolution to reach beyond proteins to highly conserved ribosomal RNA sequences, the ...
Nucleic Acids Research. 47 (17): 9024-9036. doi:10.1093/nar/gkz615. ISSN 0305-1048. PMC 6753486. PMID 31329950. " ... IV-mediated silencing as the introduction of these methyl groups by siRNAs silence both transposons and repetitive sequences of ... the siRNAs produced in this manner defend the genome against the proliferation of invading viruses and endogenous transposable ... The Arabidopsis Genome Initiative (2000). "Analysis of the genome sequence of the flowering plant Arabidopsis thaliana". Nature ...
... a leucine zipper protein involved in protein-protein interactions and a protein that binds to the terminus of nucleic acids. ... The adenine-rich sequence in LINE transcript base pairs with the cut strand to flag where the LINE will be inserted with ... Retrotransposons (also called Class I transposable elements or transposons via RNA intermediates) are a type of genetic ... Long strands of repetitive DNA can be found at each end of a LTR retrotransposon. These are termed long terminal repeats (LTRs ...
With the discovery of the nature and roles of nucleic acids in genetics, this model prompted Francis Crick's so-called Central ... PMID 15716117.[permanent dead link] Shapiro, James A. (1999). "Transposable elements as the key to a 21st century view of ... Shapiro, James A. (January 2005). "A 21st century view of evolution: genome system architecture, repetitive DNA, and natural ... the subsequently partly rejected proposal of 1970 that the direction of the flow of sequence information is only from DNA to ...
nucleic acid sequence The precise order of consecutively linked nucleotides in a nucleic acid molecule, such as DNA or RNA. ... telomere A region of repetitive nucleotide sequences at each end of a linear chromosome which protects the end of the ... translocation transposable element (TE) transversion A point mutation in which a purine nucleotide is substituted for a ... Contents: Top 0-9 A B C D E F G H I J K L M N O P Q R S T U V W X Y Z p53 palindromic sequence A nucleic acid sequence of a ...
Vassetzky NS, Kramerov DA (January 2013). "SINEBase: a database and tool for SINE analysis". Nucleic Acids Research. 41 ( ... For example, the 5' of the Alu sine is derived from 7SL RNA, a sequence transcribed by RNA Polymerase III which codes for the ... Böhne A, Brunet F, Galiana-Arnoux D, Schultheis C, Volff JN (2008). "Transposable elements as drivers of genomic and biological ... Jurka J (December 2004). "Evolutionary impact of human Alu repetitive elements". Current Opinion in Genetics & Development. 14 ...
Short tails of repetitive nucleic acids are often added to the ends of RNA molecules in order to prevent degradation, ... "Origin of a substantial fraction of human regulatory sequences from transposable elements". Trends Genet. 19 (2): 68-72. doi: ... Marguet E, Forterre P (1994). "DNA stability at temperatures typical for hyperthermophiles". Nucleic Acids Res. 22 (9): 1681- ... Nucleic Acids Research. 46 (20): 10535-45. doi:10.1093/nar/gky910. PMC 6237782. PMID 30307534. Bernstein H, Bernstein C, Michod ...
Although determining the sequence of proteins was becoming somewhat routine, methods for sequencing of nucleic acids were not ... Transposable genetic elements (transposons) are found which can replicate via transcription into an RNA intermediate which is ... In many ways, RNA folding is more highly analogous to the folding of proteins rather than to the highly repetitive folded ... At the time, "yeast nucleic acid" (RNA) was thought to occur only in plants, while "thymus nucleic acid" (DNA) only in animals ...
... a database for plant miniature inverted-repeat transposable elements". Nucleic Acids Research. 42 (1): D1176-81. doi:10.1093/ ... Though the most familiar loci of the repetitive sequences are the centromere, and the telomere, a large portion of the repeated ... P-MITE: a Plant MITE database - this database for Miniature Inverted-repeat Transposable Elements (MITEs) contains sequences ... Gelfand, Y; Rodriguez, A; Benson, G (January 2007). "TRDB--the Tandem Repeats Database". Nucleic Acids Research. 35 (Database ...
... vaginalis sequence consists of repetitive and transposable elements, reflecting a massive, evolutionarily recent expansion of ... Nucleic Acids Research. 37 (Database issue): D526-30. doi:10.1093/nar/gkn631. PMC 2686445. PMID 18824479. Conrad, Melissa D.; ... The site currently contains all of the T. vaginalis sequence project data, several EST libraries, and tools for data mining and ... 2007). "Draft Genome Sequence of the Sexually Transmitted Pathogen Trichomonas vaginalis". Science. 315 (5809): 207-12. Bibcode ...
Nucleic acid - nucleic acid regulatory sequence - nucleic acid repetitive sequence - nucleic acid sequence homology - nucleon ... DNA sequence - DNA topology - DNA transposable element - DNA virus - DNA-binding protein - dopamine D1 receptor - dopamine D2 ... amino acid - amino acid receptor - amino acid sequence - amino acid sequence homology - aminobutyric acid - ammonia - AMPA ... sequence (biology) - sequence homology - sequence motif - sequencing - serine - serotonin - serotonin receptor - serpin - ...
The ability to quickly mediate global changes is also apparent in the rapid expression of non-coding repetitive sequences. The ... 2015). "LncRNAWiki: harnessing community knowledge in collaborative curation of human long non-coding RNAs". Nucleic Acids ... Families of transposable elements-derived lincRNAs have been implicated in the regulation of pluripotency. Human pluripotency- ... Large-scale sequencing of cDNA libraries and more recently transcriptomic sequencing by next generation sequencing indicate ...
Kodama Y, Shumway M, Leinonen R (January 2012). "The Sequence Read Archive: explosive growth of sequencing data". Nucleic Acids ... Retrotransposons are transposable elements which proliferate within eukaryotic genomes through a process involving reverse ... and background noise is very low for 100 bp reads in non-repetitive regions. RNA-Seq may be used to identify genes within a ... Direct sequencing of RNA using nanopore sequencing represents a current state-of-the-art RNA-Seq technique. Nanopore sequencing ...
genome sequence did not include the interiors of highly similar repetitive elements and the extremely dense repeat regions near ... Nucleic Acids Res. 33 (20): e176. doi:10.1093/nar/gni180. PMC 1292996. PMID 16314307. Alberts, Bruce (18 November 2014). ... Alu elements are known as the most abundant type of transposable elements. Some studies have used Alu elements as a way to ... International Human Genome Sequencing Consortium (2001-02-15). "Initial sequencing and analysis of the human genome". Nature. ...
Britten, RJ; Davidson, EH (1971 Jun). "Repetitive and non-repetitive DNA sequences and a speculation on the origins of ... Nucleic Acids Research 35 (Database): D332-D338. doi:10.1093/nar/gkl828.. *↑ Glass JI, Assad-Garcia N, Alperovich N, Yooseph S ... Wessler, S. R. (13 November 2006). "Eukaryotic Transposable Elements and Genome Evolution Special Feature: Transposable ... The C. elegans Sequencing Consortium (1998). "Genome sequence of the nematode C. elegans: a platform for investigating biology" ...
... repetitive sine sequences on misaligned chromosomes and subsequently acquire mutations that cause the copy to lose the original ... Nucleic Acids Research. 41 (6): 3734-47. doi:10.1093/nar/gkt047. PMC 3616710. PMID 23376929. Roberts TC, Morris KV (December ... Those piRNAs regulate genes via the piRNA pathway in mammalian testes and are crucial for limiting transposable element damage ... A high sequence identity means that it is highly likely that these two sequences diverged from a common ancestral sequence (are ...
Subirana JA, Messeguer X (March 2010). "The most frequent short sequences in non-coding DNA". Nucleic Acids Research. 38 (4): ... Telomeres are regions of repetitive DNA at the end of a chromosome, which provide protection from chromosomal deterioration ... Hawkins JS, Kim H, Nason JD, Wing RA, Wendel JF (October 2006). "Differential lineage-specific amplification of transposable ... Non-coding DNA sequences are components of an organism's DNA that do not encode protein sequences. Some non-coding DNA is ...
Benjamini Y, Speed TP (May 2012). "Summarizing and correcting the GC content bias in high-throughput sequencing". Nucleic Acids ... This tool is able to handle alignment in repetitive regions of a genome without losing information. The output of the program ... TeXP is a Transposable Element quantification pipeline that deconvolves pervasive transcription from autonomous transcription ... SRA The Sequence Read Archive (SRA) stores raw sequence data from "next-generation" sequencing technologies including 454, ...
"siVirus: web-based antiviral siRNA design software for highly divergent viral sequences". Nucleic Acids Research. 34 (Web ... Such problems occur more frequently when the dsRNA contains repetitive sequences. It has been estimated from studying the ... Buchon N, Vaury C (February 2006). "RNAi: a defensive RNA-silencing against viruses and transposable elements". Heredity. 96 (2 ... "Nucleic Acids Research. 33 (Web Server issue): W589-91. doi:10.1093/nar/gki419. PMC 1160180. PMID 15980542.. ...
"siVirus: web-based antiviral siRNA design software for highly divergent viral sequences". Nucleic Acids Research. 34 (Web ... Such problems occur more frequently when the dsRNA contains repetitive sequences. It has been estimated from studying the ... "RNAi: a defensive RNA-silencing against viruses and transposable elements". Heredity. 96 (2): 195-202. doi:10.1038/sj.hdy. ... "Nucleic Acids Research. 33 (Web Server issue): W589-91. doi:10.1093/nar/gki419. PMC 1160180. PMID 15980542.. ...
Expression of some repetitive sequences and meiotic recombination at centromeres are repressed through methylation The entire ... Transcription reshapes methylation on the repaired gene". Nucleic Acids Research. 42 (2): 804-21. doi:10.1093/nar/gkt920. PMC ... of the genome leads to chromosome instability due to mechanisms such as loss of imprinting and reactivation of transposable ... HGMA proteins are polypeptides of ~100 amino acid residues characterized by a modular sequence organization. These proteins ...
Nucleic Acids Res. 23: 1087-1088.. OpenUrlFREE Full Text. *↵. Spertini, D., C. Beliveau and G. Bellemare, 1999 Screening of ... Functional Dissection of the Tol2 Transposable Element Identified the Minimal cis-Sequence and a Highly Repetitive Sequence in ... Functional Dissection of the Tol2 Transposable Element Identified the Minimal cis-Sequence and a Highly Repetitive Sequence in ... Functional Dissection of the Tol2 Transposable Element Identified the Minimal cis-Sequence and a Highly Repetitive Sequence in ...
We started the analysis of the Bg tritici genome with the low-pass sequencing of its genome u … ... High-Throughput Nucleotide Sequencing * Plant Diseases / microbiology * Repetitive Sequences, Nucleic Acid * Sequence Analysis ... Sequencing of the BAC ends generated 12.6 Mb of random sequence representative of the genome. Analysis of BAC-end sequences ... A major invasion of transposable elements accounts for the large size of the Blumeria graminis f.sp. tritici genome Funct ...
Repetitive Sequences, Nucleic Acid Substances * DNA Transposable Elements * Drosophila Proteins * Recombinant Fusion Proteins ... The attP sites allow the replacement of the intervening sequence of the transposon with any other sequence through recombinase- ...
The sequences flanking the Mov15 provirus were molecularly cloned and shown to consist of a tandemly repeated sequence of 31 ... DNA Transposable Elements. Gene Frequency. Mice / genetics*. Mice, Transgenic. Molecular Sequence Data. Nucleic Acid ... The repetitive sequence was also found at the subtelomeric region of three autosomes. A similar level of amplification as the ... 2575587 - Isolation of a novel mildly repetitive dna sequence that is predominantly located at th.... 15660977 - Resistance to ...
"Nucleic Acids Research. 13 (12): 4401-4410. doi:10.1093/nar/13.12.4401. PMC 321795. PMID 2409535.. ... De novo repeat identification is an initial scan of sequence data that seeks to find the repetitive regions of the genome, and ... A transposable element (TE or transposon) is a DNA sequence that can change its position within a genome, sometimes creating or ... "Nucleic Acids Res. 36 (7): 2284-94. doi:10.1093/nar/gkn064. PMC 2367713. PMID 18287116.. ...
CRISPR clusters contain sequences complementary to antecedent mobile elements and target invading nucleic acids. CRISPR ... are a family of DNA direct repeats separated by regularly sized non-repetitive spacer sequences that are found in most ... transposable elements and conjugative plasmids). ... Evolutionary conservation of sequence and secondary structures ...
Protein coding potential of retroviruses and other transposable elements in vertebrate genomes. Nucleic Acids Res 33: 946-954 ... Mouse Genome Sequencing Consortium (2002) Initial sequencing and comparative analysis of the mouse genome. Nature 420: 520-562. ... Wicker T, Robertson JS, Schulze SR et al. (2005) The repetitive landscape of the chicken genome. Genome Res 15: 126-136.PubMed ... Chimpanzee Sequencing and Analysis Consortium (2005) Initial sequence of the chimpanzee genome and comparison with the human ...
... repetitive sequences, nucleic acid MeSH G06.184.603.080.708.330 - interspersed repetitive sequences MeSH G06.184.603.080. ... 708.330.200 - dna transposable elements MeSH G06.184.603.080.708.330.200.500 - integrons MeSH G06.184.603.080.708.330.330 - ... amino acid MeSH G06.184.842.200.820 - structural homology, protein MeSH G06.184.842.550 - sequence homology, nucleic acid MeSH ... repetitive sequences, amino acid MeSH G06.184.603.060.720.030 - ankyrin repeat MeSH G06.184.603.080 - base sequence MeSH ...
Nucleic Acids Res 32 Database issue: D471-475. (2004). Rat Genome Sequencing Consortium.. "Genome sequence of the Brown Norway ... "Discovering and detecting transposable elements in genome sequences". Briefings in Bioinformatics 2007 Nov, 8(6):382-92 2006. ... "Ancestral, mammalian-wide subfamilies of LINE-1 repetitive sequences.";. J Mol Biol 246: 401-417. (1995). Smit AFA, Riggs AD. ... Nucleic Acids Res 31: 3507-3509. (2003). 2002. Zhirong Bao, Sean R. Eddy;. "Automated De Novo Identification of Repeat Sequence ...
A genome of 534 Mb was assembled from long read PacBio DNA sequencing of DNA from a highly inbred strain. Analysis of molecular ... The C. hominivorax genome was searched for repetitive DNA sequences including transposable elements. Repetitive sequences were ... Nucleic acid isolation and sequencing. High molecular weight DNA was isolated from mixed sex 6 h embryos of the inbred strain ... Repetitive DNA sequences. To identify interspersed repetitive sequences, RepeatModeler263 was used to construct a de novo ...
DNA Transposable Elements Medicine & Life Sciences * Nucleic Acid Repetitive Sequences Medicine & Life Sciences ... similar to an insertion sequence-like element. An insertion sequence-like structure was also found in a small fragment of human ... similar to an insertion sequence-like element. An insertion sequence-like structure was also found in a small fragment of human ... similar to an insertion sequence-like element. An insertion sequence-like structure was also found in a small fragment of human ...
The transposable genetic element Tn9 consists of two direct repeats of the insertion sequence IS1 flanking a region of 1,102 ... Associations of Repetitive Sequences, Nucleic Acid with chemical compounds. *Gene context of Repetitive Sequences, Nucleic Acid ... Biological context of Repetitive Sequences, Nucleic Acid. *The distribution of the middle repetitive sequences in the genome ... High impact information on Repetitive Sequences, Nucleic Acid. *Chemical compound and disease context of Repetitive Sequences, ...
Finally, the genomes of 35 C. cassiicola isolates representing the genetic diversity of the species were sequenced and ... The genome of a highly virulent C. cassiicola isolate from the rubber tree (CCP) was sequenced and assembled. In silico ... The genome of a highly virulent C. cassiicola isolate from the rubber tree (CCP) was sequenced and assembled. In silico ... 2013). Dfam: a database of repetitive DNA based on profile hidden Markov models. Nucleic Acids Res. 41, D70-D82. doi: 10.1093/ ...
There are several types: INTERSPERSED REPETITIVE SEQUENCES are copies of transposable elements (DNA TRANSPOSABLE ELEMENTS or ... "Repetitive Sequences, Nucleic Acid" by people in this website by year, and whether "Repetitive Sequences, Nucleic Acid" was a ... Repetitive Sequences, Nucleic Acid*Repetitive Sequences, Nucleic Acid. *Nucleic Acid Repetitive Sequences ... "Repetitive Sequences, Nucleic Acid" is a descriptor in the National Library of Medicines controlled vocabulary thesaurus, MeSH ...
Strand DJ, McDonald JF (June 1985). "Copia is transcriptionally responsive to environmental stress". Nucleic Acids Research. 13 ... "Computational Approaches and Tools Used in Identification of Dispersed Repetitive DNA Sequences". Tropical Plant Biol. 1: 85-96 ... A transposable element (TE, transposon, or jumping gene) is a DNA sequence that can change its position within a genome, ... When the transposable elements lack additional genes, they are known as insertion sequences. In humans, the most common TE is ...
... a program for fast and accurate assessment of transposable element presence using next-generation sequencing data NUCLEIC ACIDS ... transposable and non-transposable, repetitive and unique. Unfortunately all available nonfunctional sequences are untranscribed ... Transposable elements (TEs) are repetitive DNA sequences that are ubiquitous, extremely abundant and dynamic components of ... He-T sequences are a complex repetitive family of DNA sequences in Drosophila that are associated with telomeric regions, ...
Post-transcriptional regulation of human genes by TE-derived sequences has been observed in specific contexts, but has yet to ... We detect widespread interactions between RNA binding proteins (RBPs) and many families of TE-derived sequence in the CLIP-Seq ... Further, alignment coverage peaks on specific positions of the TE consensus sequences, illuminating a diversity of TE-specific ... Transposable elements (TEs) have significantly influenced the evolution of transcriptional regulatory networks in the human ...
Repetitive Sequences, Nucleic Acid*. Substances. *DNA Transposable Elements. *DNA, Recombinant. *DNA, Viral ... Nucleotide sequence analysis of the long terminal repeat (LTR) of avian retroviruses: structural similarities with transposable ... Sequence comparisons of the six LTRs indicate that there is conservation of sequences derived from the 5 terminus of viral RNA ... The LTR sequences were obtained from clones of unintegrated viral DNA. Comparison of these LTRs with the sequence of an ...
Repetitive Sequences, Nucleic Acid. Substance. *DNA Transposable Elements. Secondary source ID. *GENBANK/V01520 ... Structures of P transposable elements and their sites of insertion and excision in the Drosophila melanogaster genome.. OHare ... The complete DNA sequences of the 2.9 kb element and four small elements (previously isolated from hybrid-dysgenesis-induced ... The basis of this specificity has been investigated by DNA sequence analysis of the sites where 18 P elements are found. A ...
Implications for the organisation of highly repetitive, hypermethylated DNA in the genome of Physarum polycephalum. Nucleic ... DNA Sequence Analysis. DNA sequence analysis (pairwise comparisons, multiple sequence alignments, and sequence assembling and ... Diverse Roles of the Salicylic Acid Receptors NPR1 and NPR3/NPR4 in Plant Immunity ... Turcotte, K.T., Srinivasan, S., and Bureau, T. (2001). Survey of transposable elements from rice genomic sequences. Plant J. 25 ...
Implications for the organisation of highly repetitive, hypermethylated DNA in the genome of Physarum polycephalum. Nucleic ... DNA Sequence Analysis. DNA sequence analysis (pairwise comparisons, multiple sequence alignments, and sequence assembling and ... Nucleic Acids Res. 25, 4041-4047.. OpenUrlAbstract/FREE Full Text. *↵ Kumar, A., and Bennetzen, J.L. (1999). Plant ... Turcotte, K.T., Srinivasan, S., and Bureau, T. (2001). Survey of transposable elements from rice genomic sequences. Plant J. 25 ...
The spinach genome is highly repetitive with 74.4% of its content in the form of transposable elements. No recent whole genome ... Transcriptome sequencing of 120 cultivated and wild spinach accessions reveals more than 420 K variants. Our data suggests that ... Here we report the draft genome sequence of spinach (Spinacia oleracea, 2n=12), which contains 25,495 protein-coding genes. ... a program for discovering miniature inverted-repeat transposable elements from genomic sequences. Nucleic Acids Res. 38, e199 ( ...
Nucleic Acid Repetitive Sequences Medicine & Life Sciences * Transcription Initiation Site Medicine & Life Sciences ... short repetitive sequence elements. The Spm promoter is quite insensitive to the enhancer sequence of the cauliflower mosaic ... transposable element. All of the sequence required for constitutive promoter activity is confined to the 0.2-kb sequence ... short repetitive sequence elements. The Spm promoter is quite insensitive to the enhancer sequence of the cauliflower mosaic ...
... with TEs acting as platforms of regulatory sequences. Nevertheless, due to their repetitive nature it is considerably hard to ... This tool takes into account the TE sequence diversity of the genome, it can be applied to unannotated or unassembled genomes ... TEtools performs the mapping of RNA-seq data obtained from classical mRNAs or small RNAs onto a list of TE sequences and ... of the genes implicated in the piwi-interacting RNA biogenesis and therefore fits an arms race scenario between TE sequences ...
A Simplified Schematic of the Repetitive Sequence Flanking New Genes and Their Distribution over the D. melanogaster Subgroup ... Nucleic Acid*. Minor. *Animals. *Chromosome Mapping. *Chromosomes. *Computer Simulation. *DNA Transposable Elements ... Examination of their flanking sequences revealed an excess of repetitive sequences, with the majority belonging to the ... Examination of their flanking sequences revealed an excess of repetitive sequences, with the majority belonging to the ...
We annotated TE sequences from 10 fungal genomes with different TE content (1-70%). We then used these TE sequences to carry ... RIP inactivates repeated sequences by promoting Cytosine to Thymine mutations, whereas MIP only methylates TEs at C residues. ... Transposable Elements (TEs) are key components that shape the organization and evolution of genomes. Fungi have developed ... Genome-wide evidence for local DNA methylation spreading from small RNA-targeted sequences in Arabidopsis. Nucleic Acids Res. ...
... of the genome consists of repetitive sequences. The majority of the repetitive sequences are LTR-retrotransposons comprising 43 ... and annotated repetitive sequences by using a combination of next-generation sequencing (NGS) and bioinformatics tools. The ... Although the amount of sequencing data used in this study was not sufficient for a whole-genome assembly, it could generate an ... Biases in Illumina transcriptome sequencing caused by random hexamer priming.. Nucleic Acids Research 38:e131 ...
DNA transposable elements include bacterial IS (insertion sequence) elements, Tn elements, the maize controlling elements Ac ... DNA Transposable Elements: Discrete segments of DNA which can excise and reintegrate to another site in the genome. Most are ... Base Sequence*Nucleic Acid Repetitive Sequences*Interspersed Repetitive Sequences*DNA Transposable Elements: 729*Beauveria ... Base Sequence*Nucleic Acid Repetitive Sequences*Interspersed Repetitive Sequences*DNA Transposable Elements: 729*Beauveria ...
Benson G. Tandem repeats finder: a program to analyze DNA sequences. Nucleic Acids Res. 1999;27:573-580. [PMC free article] [ ... Standard methods for detecting repetitive sequence are therefore probably missing large numbers of transposable element ... Eukaryotic genomes contain millions of copies of transposable elements (TE) and other repetitive sequences. Indeed, ... repetitive sequence (after false-positive control), mostly from copies of transposable elements. The compatibility of results ...
2014 Illumina TruSeq synthetic long-reads empower de novo assembly and resolve complex, highly-repetitive transposable elements ... and TART-related sequences. Nucleic Acids Res. 27: 3318-3324. ... 2009 Novel sequencing strategy for repetitive DNA in a ... Note that the sequences of Mst77Y genes deposited in 2010 (GQ868243−GQ868260) correspond to their coding sequences and hence ... To circumvent PCR-induced artifacts Krsticevic et al. (2010) sequenced more than 100 clones and only picked gene sequence ...
  • The Tol2 element is a naturally occurring active transposable element found in vertebrate genomes. (genetics.org)
  • Clustered Regularly Interspaced Short Palindromic Repeats (CRISPR) are a family of DNA direct repeats separated by regularly sized non-repetitive spacer sequences that are found in most bacterial and archaeal genomes [ PMID: 17442114 ]. (ebi.ac.uk)
  • Finally, the genomes of 35 C. cassiicola isolates representing the genetic diversity of the species were sequenced and assembled, and putative effectors identified. (frontiersin.org)
  • We isolated and measured the fitness of thousands of independent adaptive clones and sequenced the genomes of hundreds of clones. (stanford.edu)
  • Transposable Elements (TEs) are key components that shape the organization and evolution of genomes. (biomedcentral.com)
  • Transposable elements (TEs) are mobile genetic element able to transpose and multiply in genomes. (biomedcentral.com)
  • Over recent decades, substantial efforts have been made to understand the interactions between host genomes and transposable elements (TEs). (inria.fr)
  • This tool takes into account the TE sequence diversity of the genome, it can be applied to unannotated or unassembled genomes and is freely available under the GPL3 (https://github.com/l-modolo/TEtools). (inria.fr)
  • Transposable elements (TEs) are conventionally identified in eukaryotic genomes by alignment to consensus element sequences. (pubmedcentralcanada.ca)
  • Eukaryotic genomes contain millions of copies of transposable elements (TE) and other repetitive sequences. (pubmedcentralcanada.ca)
  • Indeed, approximately half of the sequence content of typical mammalian genomes tends to be annotated as TEs and simple repeats by conventional annotation methods. (pubmedcentralcanada.ca)
  • Transposable Elements (TE) are mobile sequences that make up large portions of eukaryote genomes. (biomedcentral.com)
  • Recombination-driven deletions and minimal transposable element (TE) expansions have led to continually shrinking genomes during evolution of many lineages of volant birds. (deepdyve.com)
  • Widespread evidence for horizontal transfer of transposable elements across Drosophila genomes. (geneticsmr.com)
  • Transposable elements (TEs) are mobile sequences found in nearly all eukaryotic genomes. (biomedcentral.com)
  • The number of sequenced genomes is rapidly rising, and the need to identify TEs within them is also growing. (biomedcentral.com)
  • In this work, we describe a homology-based approach for the automatic identification of high-quality consensus TEs, aimed for use in the analysis of newly sequenced genomes. (biomedcentral.com)
  • We apply our approach to newly sequenced genomes and successfully identify consensus TEs that are up to 99% identical to manually annotated TEs. (biomedcentral.com)
  • Transposable elements (TEs) are a type of repetitive sequence that have been found in nearly all eukaryotic genomes. (biomedcentral.com)
  • Here we present a comprehensive map of 7,380 MEI polymorphisms from the 1000 Genomes Project whole-genome sequencing data of 185 samples in three major populations detected with two detection methods. (prolekare.cz)
  • Retrotransposons are endogenous genomic sequences that copy and paste into locations throughout host genomes [1] - [3] . (prolekare.cz)
  • The genome-wide patterns of sequence diversity of the active autonomous TEs in the genomes of D. melanogaster , D. simulans and D. yakuba suggest that one-third of the TE families originated by recent HT between these species. (beds.ac.uk)
  • Transposable Elements (TEs) make up the majority of plant genomes, and thus understanding TE evolutionary dynamics is key to understanding plant genome evolution. (biomedcentral.com)
  • The number of Numts in chicken is low compared to those in human and plant genomes, and is within the range found for most sequenced eukaryotic genomes. (biomedcentral.com)
  • Metabolic selection for compact genomes with reduced repetitive DNA and gene-poor regions where Numts occur may explain their low incidence in birds. (biomedcentral.com)
  • We identified miRNAs in many of the first-sequenced plant genomes, investigating miRNA diversity and biogenesis, and characterizing plant miRNA evolution. (missouri.edu)
  • In this study, we systematically identified and analyzed PHIS transposons in 836 sequenced eukaryotic genomes using transposase homology search and structure approach. (biomedcentral.com)
  • TEs not only have significant impact on the evolution of the host genomes and biological complexity but also are challenges for host genome sequencing, assembly, and annotation due to their repeatability. (biomedcentral.com)
  • Here, we systematically identified and analyzed PHIS transposons in 836 sequenced eukaryotic genomes using transposase homology search combined with structure approach. (biomedcentral.com)
  • it involves the creation of electronic data bases on genomes, protein sequences, etc. (kumc.edu)
  • A large portion of plant genomes accounts for repetitive DNA [ 5 - 8 ]. (hindawi.com)
  • Eukaryotic genomes contain a large proportion of repetitive DNA sequences, mostly transposable elements (TEs) and tandem repeats. (biomedsearch.com)
  • These sequences provide useful retrospective information about ancient retroviruses, and have also played an important role in shaping the evolution of vertebrate genomes. (biomedcentral.com)
  • Transposable elements are ubiquitous components of all genomes. (biomedcentral.com)
  • In plants, TEs comprise up to 80% of the genomes, with prevailing long terminal repeat (LTR) families of Ty1- copia and Ty3- gypsy retrotransposons [ 2 , 3 ], which vary extensively in their sequence motifs and abundances, even between closely related species [ 4 , 5 ]. (hindawi.com)
  • Following recent developments in genome sequencing and the availability of a wealth of new genomes, Tc1/mariner TEs have been identified in many new taxa across the eukaryotic tree of life. (biomedcentral.com)
  • Mammalian transposable elements have been restructuring their host genomes for millions of years, to both deleterious and advantageous effects. (bioscience.org)
  • While the total number of cellular genes has remained relatively conserved in the course of mammalian evolution, the genomic mass occupied by transposable elements populating mammalian genomes has grown up to as much as 52% (58,65,79,94,119,126). (bioscience.org)
  • Cut-and-paste DNA transposable elements are major components of eukaryotic genomes and are grouped into superfamilies (e.g., hAT , P ) based on sequence similarity of the element-encoded transposase. (pnas.org)
  • Analysis of such sequences across 12 Drosophila genomes showed that the occurrence of repetitive sequences in the context of boundaries is a common feature of drosophilids. (omictools.com)
  • Transposable elements (TEs) are a rapidly evolving fraction of the eukaryotic genomes and the main contributors to genome plasticity and divergence. (beds.ac.uk)
  • We demonstrated that Tol2 vectors with 200 bp from the left end and 150 bp from the right end were capable of transposition without reducing the transpositional efficiency and found that these sequences, including the terminal inverted repeats (TIRs) and the subterminal regions, are sufficient and required for transposition. (genetics.org)
  • Transposons are typically bounded by terminal inverted repeats (TIRs), which flank and serve as the recognition sequence for the transposase. (biomedcentral.com)
  • Genome analysis also revealed new features such as the presence of segmental duplications of up to 16 kb flanked by inverted repeats, and the tight association of some gene families with transposable elements. (pubmedcentralcanada.ca)
  • Here we report the draft genome sequence of spinach ( Spinacia oleracea , 2n=12), which contains 25,495 protein-coding genes. (nature.com)
  • Post-transcriptional regulation of human genes by TE-derived sequences has been observed in specific contexts, but has yet to be systematically and comprehensively investigated. (biomedcentral.com)
  • Previous studies of repetitive elements (REs) have implicated a mechanistic role in generating new chimerical genes. (nih.gov)
  • Examination of their flanking sequences revealed an excess of repetitive sequences, with the majority belonging to the transposable element DNAREP1 family, associated with the new genes. (nih.gov)
  • The impact of TEs on the regulation of host genes is well known, with TEs acting as platforms of regulatory sequences. (inria.fr)
  • Our data show for the first time that the activity of TEs is strictly linked to the activity of the genes implicated in the piwi-interacting RNA biogenesis and therefore fits an arms race scenario between TE sequences and host control genes. (inria.fr)
  • The Mst77Y genes were severely misassembled in the then-available genome assembly and were identified by cloning and sequencing polymerase chain reaction products. (g3journal.org)
  • The PacBio MHAP assembly of the Mst77Y region seems to be very accurate, as revealed by comparisons with the previously found Mst77Y genes, a bacterial artificial chromosome sequence, and Illumina reads of the same strain. (g3journal.org)
  • used a de novo sequencing approach, polymerase chain reaction (PCR) of Mst77Y -like genes followed by cloning and sequencing, and found 18 Mst77Y genes. (g3journal.org)
  • They also used two other methods that yielded similar estimates of the number of Mst77Y genes: restriction enzyme digestion plus band quantification (16 copies) and computational analysis of the whole-genome sequencing traces (14 copies). (g3journal.org)
  • Differential expression analyses identified 396 candidate genes among divergent animals for intramuscular fatty acid composition. (biomedcentral.com)
  • Pathway analysis related these genes to biological functions and canonical pathways controlling lipid and fatty acid metabolisms. (biomedcentral.com)
  • The nucleotide sequence of Protobothrops flavoviridis (Pf) 30534 bp genome segment which contains genes encoding small serum proteins (SSPs) was deciphered. (elsevier.com)
  • The genome segment contained five SSP genes (PfSSPs), PfSSP-4, PfSSP-5, PfSSP-1, PfSSP-2, and PfSSP-3 in this order and had characteristic configuration and constructions of the particular nucleotide sequences inserted. (elsevier.com)
  • and insertions into genes and other functional sequences are typically eliminated by natural selection. (peerj.com)
  • Scaffolds and chromosomes are connected to the NRRL 3357 chromosomes by lines representing high sequence similarity between two protein-coding genes. (springer.com)
  • The hidden transcriptome , revealed by run-on transcription of genes or repetitive elements, contains a diverse repertoire of RNA immune receptors , with the potential to form double-stranded RNA with viral RNA antigens , thus triggering intracellular alarms. (queensu.ca)
  • We predicted 10,847 protein coding genes, and identify 479 of these undergoing positive directional selection with the use of population genetic analysis based on low-coverage whole genome sequencing of 19 individuals. (g3journal.org)
  • CG island Unmethylated cytosine-guanine sequences that are often found near the 5' ends of some genes. (kumc.edu)
  • The amino acid sequences of proteins are encoded in the genes. (nap.edu)
  • We have been linking a number of these disease genes to repetitive sequences and the maintenance of X-inactivation. (umn.edu)
  • In non-recombining regions of the Y chromosome repetitive DNA sequences are accumulated, representing a dominant and early process forming the Y chromosome, probably before genes start to degenerate. (biomedsearch.com)
  • Functional classification of 60% of the genes was modified based on recent sequence comparisons and new experimental data. (pubmedcentralcanada.ca)
  • Whole-genome sequencing revealed brain-specific L1 insertion in patients localized preferentially to synapse- and schizophrenia-related genes. (scienceoveracuppa.com)
  • The complex polyploid nature of the genome of bread wheat, Triticum aestivum , and the technically difficult task of sequencing clusters of tandem repeats mean that the detailed organization of extended genomic regions containing 5S rRNA genes remains unclear. (biomedcentral.com)
  • The function of repetitive DNA was illuminated by several lines of genome research showing showing that repetitive DNA is an evolutionary device to catalyze formation of new genes by suppressing gene conversion. (freeshell.org)
  • Repetitive sequences play the role of uncoupling this network, thereby allowing new genes to evolve. (freeshell.org)
  • Analysis of the complete BAC_2383A24 nucleotide sequence (113 605 bp) demonstrated that it contains 55.6% TEs, 0.9% subtelomeric tandem repeats (Spelt1), and five genes. (beds.ac.uk)
  • that have mutations or deletions in the transposase gene, but retain essential cis -sequences, and can transpose in the presence of the transposase activity. (genetics.org)
  • Here we show that in division I strains the capsulation (cap) gene cluster lies between direct repeats of a novel insertion sequence (IS)-like element, IS1016. (nih.gov)
  • During vertebrate evolution, transposable elements have repeatedly contributed regulatory and coding sequences to the host, leading to the emergence of new lineage-specific gene regulations and functions. (springer.com)
  • Repetitive element-mediated recombination as a mechanism for new gene origination in Drosophila. (nih.gov)
  • They shape the genomic landscape by providing novel DNA sequences at various locations, by contributing to chromosomal rearrangements, gene duplications, gene loss and inactivation and by accelerating evolution. (biomedcentral.com)
  • Russell and Kaiser (1993) found three Y-linked pseudogenes of this gene ( Mst77 -ψ1, Mst77 -ψ2, and Mst77 -ψ3) by sequencing testis complementary DNAs. (g3journal.org)
  • Because the DNA came from an inbred strain (the same used in genome sequencing), each different gene sequence variant was inferred to correspond to a different gene. (g3journal.org)
  • sequenced more than 100 clones and only picked gene sequence variants occurring twice or more. (g3journal.org)
  • Goggins LW, Vass JK, Stinson MA, Lanyon WG, Paul J (1982) A B1 repetitive sequence near the mouse β-major globin gene. (springer.com)
  • Koop BF, Miyamoto MM, Embury JE, Goodman M, Czelusniak J, Slightom JL (1986) Nucleotide sequences and evolution of the orangutan epsilon globin gene region and surrounding Alu repeats. (springer.com)
  • We recently reported the genome and transcriptome sequencing of A. flavus WRRL 1519, a strain isolated from almond that does not produce aflatoxins or cyclopiazonic acid due to deletions in the biosynthetic gene clusters. (springer.com)
  • In contrast, the S-locus region itself shows spectacularly deep gene genealogies, high variability in size and gene organization, as well as complete absence of sequence similarity in intergenic sequences and striking accumulation of transposable elements. (prolekarniky.cz)
  • Chromatin Human chromosomal DNA is packaged into a string of distinct protein-nucleic acid complexes, called chromatin structures, which are critical for gene regulation, genome stability, and protection against cancer. (umn.edu)
  • In the laboratory of Edward Rubin at the University of California, Berkeley, postdoctoral fellow Nadav Ahituv combined the human version of the LF-SINE sequence with a "reporter" gene that would produce an easily recognizable protein if the LF-SINE were serving as its on-off switch. (creation.com)
  • Many of those sequences were located in gene deserts, which are in fact so clogged with regulatory DNA elements that they have recently been renamed regulatory jungles . (creation.com)
  • We determined the genome of L. corymbifera (formerly Mycocladus corymbifer ex Absidia corymbifera ) and found high dissimilarities between L. corymbifera and other sequenced mucoralean fungi in terms of gene families and syntenies. (plos.org)
  • We have corrected the sequence assembly, improved the gene predictions and refreshed the functional gene assignments. (pubmedcentralcanada.ca)
  • As a result, this effort has led to a more accurate gene annotation, and the discovery of novel features, such as the presence of genome segmental duplications and the close association of some gene families with transposable elements. (pubmedcentralcanada.ca)
  • Historically the accumulated mass of mammalian transposable elements (TEs), particularly those located within gene boundaries, was viewed as a genetic burden potentially detrimental to the genomic landscape. (bioscience.org)
  • TE-induced changes in gene expression can be tissue- or disease-specific, raising the possibility that the impact of TE sequences may vary during development, among normal cell types, and between normal and disease-affected tissues. (bioscience.org)
  • While the disruption of normal gene function by transposable elements upon integration into exonic regions is obvious, their post-insertional effects on gene expression have not received much attention. (bioscience.org)
  • The appreciation for TE modification of mammalian gene expression gained significant interest after the discoveries that the majority of transposable elements either carry cis -acting elements in their sequence that are recognized by the mammalian transcriptional or RNA processing machineries or have high propensity for accrual of these cis -signals via mutations long after the completion of the integration process. (bioscience.org)
  • The internal transcribed spacer 2 (ITS2) of the 45S rRNA gene was sequenced for micro B, large B, and A chromosomes of B. dichromosomatica cytodeme A2, and conserved differences were identified between sequences originating from A and both types of B chromosomes. (jove.com)
  • The insertion of repetitive transposable DNA sequence, SINEs and LINEs acts to break up DNA homologies and allow new gene variations to evolve The evidence has been gathered here so that a new generation of genomic scientists may examine it in the fresh light of reason. (freeshell.org)
  • Gene conversion links similar DNA sequences together. (freeshell.org)
  • Similar DNA sequences are the substates for gene conversion. (freeshell.org)
  • The gene pool of a species consists of DNA sequences in a network linked by gene conversion events. (freeshell.org)
  • The shorter Alu or SINE repetitive DNA are specialized for uncoupling intrachromosomal gene conversion while the longer LINE repetitive DNA are specialized for uncoupling interchromosomal gene conversion. (freeshell.org)
  • We sequenced the most virulent isolate, the first full genome sequences of H. parviporum as a reference genome, and re-sequenced the remaining 14 H. parviporum isolates. (beds.ac.uk)
  • To directly address this issue, we extracted and compared the DNA sequences of all autonomous TEs in the genome sequences of D . melanogaster , D. simulans and D. yakuba . (beds.ac.uk)
  • We took advantage of the recent availability of genome sequences for a wide range of species to investigate the mechanism underlying genome size equilibrium over the past 100 million years. (pnas.org)
  • 500 eukaryotic genome sequences are available in public repositories, the majority are highly fragmented with incomplete assemblies, which explains why considerable effort and resources are often spent to improve their quality after publication. (plos.org)
  • TRANSPOSONS are genetic elements that move from one locus to another locus and reside in the genome as repetitive sequences. (genetics.org)
  • A transposable element ( TE or transposon ) is a DNA sequence that can change its position within a genome , sometimes creating or reversing mutations and altering the cell's genetic identity and genome size . (wikipedia.org)
  • Transposable elements represent one of several types of mobile genetic elements . (wikipedia.org)
  • CRISPRs appear to provide acquired resistance against mobile genetic elements (viruses, transposable elements and conjugative plasmids). (ebi.ac.uk)
  • 2005) Transposable elements as a source of genetic innovation: expression and evolution of a family of retrotransposon-derived neogenes in mammals. (springer.com)
  • These sequences provide insights into the structure and evolution of the spinach genome, the phylogeny and genetic diversity of spinach populations, genomic signatures underlying spinach domestication, and the underlying molecular basis of specific agronomically important traits. (nature.com)
  • These structural analogies include the presence of inverted complementary repeats at the termini of the LTR, deletions adjacent to LTR termini, and sequence homologies with transposable and other genetic elements. (nih.gov)
  • These results will help in the identification of genetic variants at loci that affect fatty acid composition traits. (biomedcentral.com)
  • Complete nucleotide sequence and genome organization of a Drosophila transposable genetic element, 297. (geneticsmr.com)
  • The view that multicellular immune systems are adaptations of already highly evolved unicellular immune systems that are capable of self/not-self discrimination can assist our comprehension of phenomena such as junk DNA, genetic polymorphism and the ubiquity of repetitive elements. (queensu.ca)
  • Self-incompatibility has been considered by geneticists a model system for reproductive biology and balancing selection, but our understanding of the genetic basis and evolution of this molecular lock-and-key system has remained limited by the extreme level of sequence divergence among haplotypes, resulting in a lack of appropriate genomic sequences. (prolekarniky.cz)
  • The orderly sequence of events in which a cell duplicates its contents, including its genetic material, and divides into two cells. (nap.edu)
  • We used long-read sequencing augmented by transcriptomics, optical and genetic mapping along with shared synteny from closely related fish species to derive a chromosome-level assembly with a contig N50 size over 1 Mb and scaffold N50 size over 25 Mb that span ~90% of the genome. (plos.org)
  • In our study, we employed long read sequencing combined with genetic and optical mapping, and syntenic information to produce a chromosomal level assembly. (plos.org)
  • Complete genome sequencing of Leptospira interrogans serovar Copenhageni and comparative analysis with the available Leptospira interrogans serovar Lai genome reveal that despite overall genetic similarity there are significant structural differences, including a large chromosomal inversion and extensive variation in the number and distribution of insertion sequence elements. (asm.org)
  • Recent research has highlighted the potential role of transposable elements (TE) in the genetic instability of certain psychiatric and neurodevelopmental conditions, such as schizophrenia and autism. (scienceoveracuppa.com)
  • Structure and chromosomal mapping of a highly polymorphic repetitive DNA sequence from the pseudoautosomal region of the mouse sex chromosomes. (biomedsearch.com)
  • Ma H, Reyes-Gutierrez P, Pederson T. Visualization of repetitive DNA sequences in human chromosomes with transcription activator-like effectors. (umassmed.edu)
  • PacBio genome sequence analyses of putative centromeric regions on C. arabica and C. canephora chromosomes showed an exceptional density of one family of CRC elements, and the complete absence of satellite arrays, contrasting with usual structure of plant centromeres. (frontiersin.org)
  • Artificial nucleotides such as bridged nucleic acids ( BNAs ) have been described for the development of chimeric BNA/DNA oligonucleotides as probes for fluorescence in situ hybridization on metaphase chromosomes and interphase nuclei. (blog-biosyn.com)
  • Satellite 2 (Sat2) DNA sequences are found predominantly in juxtacentromeric heterochromatin of certain human chromosomes and are most abundant in the long juxtacentromeric heterochromatin region of chromosome (Chr) 1. (blog-biosyn.com)
  • It allows the detection and precise localization of repetitive or single-copy sequences on interphase nuclei, chromosomes in mitosis and meiosis or chromatin fibers. (hindawi.com)
  • The role of repetitive DNA in structure and evolution of sex chromosomes in plants. (biomedsearch.com)
  • These repetitive sequences often colonize specific chromosomal (Y or W chromosomes, B chromosomes) or subchromosomal (telomeres, centromeres) niches. (biomedsearch.com)
  • Little is known about these early steps, but an accumulation of transposable element sequences has been observed on the Y-chromosomes of some species with heteromorphic sex chromosomes. (biomedcentral.com)
  • Recombination, by which transposable elements are removed, is suppressed on at least part of the emerging Y-chromosome, and this may explain the correlation between the emergence of sex chromosomes and transposable element enrichment. (biomedcentral.com)
  • We detect widespread interactions between RNA binding proteins (RBPs) and many families of TE-derived sequence in the CLIP-Seq data. (biomedcentral.com)
  • When the polymorphism affects proteins, it probably affects sequences of relatively low complexity that correspond to hydrophilic non-globular domains at the protein surface [7]. (queensu.ca)
  • Proteins consist of one or more chains of amino acids called polypeptides. (nap.edu)
  • These proteins have a high proportion of positively charged amino acids (lysine and arginine) and they bind tightly to the negatively charged DNA. (flashcardmachine.com)
  • Regulatory proteins that bind to specific sequences or structures within the untranslated region at the 5' end of the mRNA, preventing the attachment of ribosomes. (flashcardmachine.com)
  • Pederson T. Repeated TALEs: visualizing DNA sequence localization and chromosome dynamics in live cells. (umassmed.edu)
  • We found that the Mst77Y region spans 96 kb and originated from a 3.4-kb transposition from chromosome 3L to the Y chromosome, followed by tandem duplications inside the Y chromosome and invasion of transposable elements, which account for 48% of its length. (g3journal.org)
  • The sequence mapping and FISH experiments of CRC Reverse Transcriptase domains in C. canephora, C. eugenioides , and C. arabica clearly indicate a strong and specific targeting mainly onto proximal chromosome regions, which can be associated also with heterochromatin. (frontiersin.org)
  • By comparative multicolor FISH, we have physically mapped small chromosome fragments in the sugar beet addition lines PRO1 and PAT2 and analyzed the distribution of repetitive DNA families in species of the section Procumbentes of the genus Beta . (hindawi.com)
  • Role of the Xist locus and repetitive sequences in X-inactivation and X chromosome stability. (umn.edu)
  • It therefore appears that Xist maintains repetitive sequences along the X chromosome in a stabilizing heterochromatin structure and we are examining this in more detail. (umn.edu)
  • Here we review the occurrence and role of repetitive DNA in Y chromosome evolution in various species with a focus on dioecious plants. (biomedsearch.com)
  • We sequenced 2321 bp of the Y-chromosome in Bryonia dioica that flank a male-linked marker, BdY1 , reported previously. (biomedcentral.com)
  • An empirical correlation observed is the accumulation of transposable elements and other repetitive sequences on the Y- (or W-) chromosome [ 10 ]. (biomedcentral.com)
  • Using the results of pyrosequencing and assembling, we obtained six 5S rDNA- containing contigs with a total length of 140,417 bp, and two sets (pools) of individual 5S rDNA sequences belonging to separate, but closely located genomic regions on the 5BS chromosome. (biomedcentral.com)
  • Phylogenetic analysis did not identify a species containing an ITS2 sequence more similar to either of the B chromosome sequences than the B. dichromosomatica A chromosome sequences. (jove.com)
  • There are several types: INTERSPERSED REPETITIVE SEQUENCES are copies of transposable elements (DNA TRANSPOSABLE ELEMENTS or RETROELEMENTS) dispersed throughout the genome. (umassmed.edu)
  • Mobilization of transposable elements (TEs) is a DNA recombination reaction that can occur either via RNA (retroelement/retrovirus) or DNA intermediates (DNA transposon). (prolekare.cz)
  • Within this region, which should be suppressed for recombination, we observed a solo-LTR nested in a Copia -like transposable element. (biomedcentral.com)
  • However, the circumstances that increase transcription and insertion of active mobile elements likewise destabilize their extinct predecessors and other repetitive sequences within the genome, leading to a variety of mutational events, such as nonallelic homologous recombination of low copy repeats (LCR). (scienceoveracuppa.com)
  • The forces behind this variation are not fully understood, although one of the obvious explanations is a potential difference in the rate of TE buildup through mobilization in any given genome and loss of accumulated TE sequences due to recombination. (bioscience.org)
  • Bucheton A (1990) I transposable elements and I-R hybrid dysgenesis in Drosophila . (springer.com)
  • Structures of P transposable elements and their sites of insertion and excision in the Drosophila melanogaster genome. (nih.gov)
  • We have isolated and characterized several members of the P transposable element family from a Drosophila melanogaster P strain. (nih.gov)
  • DNA transposable elements include bacterial IS (insertion sequence) elements, Tn elements, the maize controlling elements Ac and Ds, Drosophila P, gypsy, and pogo elements, the human Tigger elements and the Tc and mariner elements which are found throughout the animal kingdom. (curehunter.com)
  • Using cdBEST, we identified boundary sequences across 12 Drosophila species. (omictools.com)
  • Of the 4576 boundary sequences identified in Drosophila melanogaster genome, >170 sequences are repetitive in nature and have sequence homology to transposable elements. (omictools.com)
  • Functional Dissection of the To12 Transposable Element Identified the Minimal cis-Sequence and a Highly Repetitive Sequence in the Subterminal Region Essential for Transportation", Genetics Society of America, Oct. 2006, vol. 174. (freepatentsonline.com)
  • The Tol1 transposable element of the medaka fish moves in human and mouse cells", Journal of Human Genetics, 2007, vol. 52, pp. 628-635. (freepatentsonline.com)
  • Feschotte C, Jiang N, Wessler S (2002) Plant transposable elements: where genetics meets genomics. (springer.com)
  • It also talks about a few applications of this family of transposable element in forward and reverse genetics. (asmscience.org)
  • Polymorphic bands can even be excised from the gel and sequenced. (wikimd.org)
  • To identify polymorphic MEIs (pMEIs), both targeted and next-generation sequencing (NGS) analysis have been developed. (biomedcentral.com)
  • The oyster genome is highly polymorphic and rich in repetitive sequences, with some transposable elements still actively shaping variation. (ox.ac.uk)
  • The former is highly conserved in structure, whereas the NTS is polymorphic in both length and nucleotide sequence. (biomedcentral.com)
  • We demonstrate here that approximately half of this uncharted territory is in fact comprised of repetitive or repeat-derived sequences, which are most likely dominated by transposable elements. (pubmedcentralcanada.ca)
  • Transposable element annotation of the rice genome. (repeatmasker.org)
  • These results highlight the need for combined, probabilistic genome annotation approaches and suggest that the human genome consists of substantially more repetitive sequence than previously believed. (pubmedcentralcanada.ca)
  • Annotation, submission and screening of repetitive elements in Repbase: repbasesubmitter and censor. (geneticsmr.com)
  • Because high-throughput genome sequencing technology has become widely available, many genome projects are now carried out by small groups with little prior experience in genome annotation. (plantphysiol.org)
  • Our results not only enrich the transposon diversity but also have extensive significance for improving genome sequence assembly and annotation of higher organisms. (biomedcentral.com)
  • The program outputs a detailed annotation of the repeats that are present in the query sequence (represented by this track), as well as a modified version of the query sequence in which all the annotated repeats have been masked (generally available on the Downloads page). (ucsc.edu)
  • Transcriptome sequencing of 120 cultivated and wild spinach accessions reveals more than 420 K variants. (nature.com)
  • Here we report a high-quality genome assembly of a Chinese spinach cultivar, Sp75, in addition to transcriptome sequences of 120 cultivated and wild spinach accessions. (nature.com)
  • Evidence of binding and conservation of these motifs in the nonrepetitive transcriptome suggests that TEs have generally appropriated existing sequence preferences of the RBPs. (biomedcentral.com)
  • With this in mind, we have used massive, parallel high-throughput sequencing technologies to characterize the porcine adipose tissue transcriptome architecture in six Iberian x Landrace crossbred pigs showing extreme phenotypes for intramuscular fatty acid composition (three per group). (biomedcentral.com)
  • High-throughput RNA sequencing was used to generate a whole characterization of adipose tissue (backfat) transcriptome. (biomedcentral.com)
  • In this study, we used a next-generation sequencing (NGS) approach to investigate the plant responses to the co-infection of CTV and CDVd in two commercial grapefruit ( Citrus paradisi ) cultivars, on both the sRNA and transcriptome level. (biomedcentral.com)
  • This notion has been strengthened by the discovery that transposable sequences can alter the architecture of the transcriptome, not only through insertion, but also long after the integration process is completed. (bioscience.org)
  • CRISPR clusters contain sequences complementary to antecedent mobile elements and target invading nucleic acids. (ebi.ac.uk)
  • A nucleotide sequence that is complementary to a sequence ofmessenger RNA (mRNA). (wikimd.org)
  • Krayev AS, Kramerov DA, Skryabin KG, Ryskov AP, Bayev AA, Georgiev GP (1980) The nucleotide sequence of the ubiquitous repetitive DNA sequence B1 complementary to the most abundant class of fold-back RNA. (springer.com)
  • Compared to locked nucleic acids (LNAs) the substitution of DNA monomers with BNA monomers in oligonucleotides adds exceptional biological stability, resistance to nucleases and a significantly increased affinity to their complementary DNA targets. (blog-biosyn.com)
  • small, single stranded RNA molecules that bind to complementary sequences in mRNA molecule. (flashcardmachine.com)
  • The nucleotide sequences of the long terminal repeat (LTR) from six independently derived avian retrovirus recombinant DNA clones have been determined. (nih.gov)
  • A Novel Abundant Family of Transposable Elements (DAS-SINEs) in The Nine-Banded Armadillo (Dasypus novemcinctus). (repeatmasker.org)
  • Kramerov DA, Grigoryan AA, Ryskov P, Georgiev GP (1979) Long double-stranded sequences (ds RNA-B) of nuclear pre-mRNA consist of a few highly abundant classes of sequences: evidence from DNA cloning experiments. (springer.com)
  • The most abundant short interspersed nucleotide element (SINE) in human DNA is the Alu repeat, an ~282 bp non-LTR (Long Terminal Repeat) DNA sequence, which comprises 10% of the human genome and is present in ~1 million copies per haploid genome. (blog-biosyn.com)
  • Other abundant non-LTR sequences are long interspersed nucleotide elements (LINEs) of up to 6 kb that comprise ~20% of the human genome. (blog-biosyn.com)
  • However, most Alu sequences in the genome are members of abundant, formerly active, subfamilies that are now transpositionally inert. (peerj.com)
  • Repetitive content makes up more than one-third of this genome, and previously uncharacterized transposable elements are the most abundant type of repetitive DNA. (g3journal.org)
  • The most abundant transposable elements in the chicken genome (approximately 80%) belong to the CR1 families of LINE retrotransposons (Chicken Repetitive 1 Elements or CR1). (beds.ac.uk)
  • Evolutionary conservation of sequence and secondary structures in CRISPR repeats. (ebi.ac.uk)
  • Taken together, these observations indicate that transposable elements are major drivers of genomic and biological diversity in vertebrates, with possible important roles in speciation and major evolutionary transitions. (springer.com)
  • MEGA: a biologist-centric software for evolutionary analysis of DNA and protein sequences. (geneticsmr.com)
  • However, methodological issues such as ascertainment bias (for example, the use of TE detection methods based on sequence homology, such as PCR or nucleotide sequence comparisons, or the preferential study of young active TE families) mean that this catalogue of HT cases cannot be used as a reference for the relative importance of such events in the evolutionary biology of the pool of active elements in a given genome. (beds.ac.uk)
  • Jurka J (2004) Evolutionary impact of human Alu repetitive elements. (springer.com)
  • Taking the data together, this study suggests that all eukaryotic cut-and-paste transposable element superfamilies have a common evolutionary origin and establishes a phylogenetic framework for all future cut-and-paste transposase comparisons. (pnas.org)
  • Contained within the transforming fragment are sequences that can be drawn as a stem-loop structure flanked by direct repeats, similar to an insertion sequence-like element. (elsevier.com)
  • An insertion sequence-like structure was also found in a small fragment of human cytomegalovirus DNA that has transforming activity. (elsevier.com)
  • Galloway, DA , Nelson, JA & McDougall, JK 1984, ' Small fragments of herpesvirus DNA with transforming activity contain insertion sequence-like structures ', Proceedings of the National Academy of Sciences of the United States of America , vol. 81, no. 15 I, pp. 4736-4740. (elsevier.com)
  • P elements have 31 bp perfect inverse terminal repeats and upon insertion duplicate an 8 bp sequence found only once at the site of insertion. (nih.gov)
  • A 128-bp insertion into the maize waxy-B2 allele led to the discovery of Tourist , a family of miniature inverted repeat transposable elements (MITEs). (plantcell.org)
  • Such a determination is possible only with a systematic comparison between the insertion frequency of MITEs into MITEs and of MITEs into other sequences. (plantcell.org)
  • In 1990, a bacterial insertion sequence found in the Shigella genome, IS630, was linked to Tc1 , as it shares a TA target site duplication (TSD) formed after successful transposition [ 7 ]. (biomedcentral.com)
  • In particular, L1 elements exhibit a variety of sequence structures after insertion into the human genome that are amenable to computational analysis. (beds.ac.uk)
  • The sequence data give no indication that the creation of L1 structural variants depends on characteristics of the insertion locus. (beds.ac.uk)
  • (c) TSD sequences flanking an L1 insertion are underlined. (beds.ac.uk)
  • Although the amount of sequencing data used in this study was not sufficient for a whole-genome assembly, it could generate an overview of representative elements in the genome. (peerj.com)
  • We have developed an algorithm, called Mobster, to detect non-reference mobile element insertions in next generation sequencing data from both whole genome and whole exome studies. (biomedcentral.com)
  • Comparative analyses of multi-species sequences from targeted genomic regions. (repeatmasker.org)
  • d) Divergence curves of select CR1 families based on BLASTing raw TE matches to a portion of the 3 end of species- and TE-specific consensus sequences (see supplementary table S1, Supplementary Material online). (deepdyve.com)
  • In this study, we report and analyze the full sequence of eleven distinct haplotypes of the self-incompatibility locus (S-locus) in two closely related Arabidopsis species, obtained from individual BAC libraries. (prolekarniky.cz)
  • We sequenced, assembled, and annotated a high-quality draft genome of 299.6 Mbp for this species. (g3journal.org)
  • However, genome sequencing has revealed that many mammal and bird lineages have experienced differential rates of transposable element (TE) accumulation, which would be predicted to cause substantial variation in genome size between species. (pnas.org)
  • They evolve rapidly in copy number resulting in species-specific variants and/or novel sequence families [ 10 ] and are thus crucial for genome evolution [ 11 ]. (hindawi.com)
  • The population structure of L . calcarifer species complex was analyzed by re-sequencing 61 individuals representing various regions across the species' native range. (plos.org)
  • In addition, population structure of the species was analysed based on low-coverage genome sequence information from 61 individuals representing diverse geographic locations stretching from North-Western India across South-East Asia and Australia to Papua New Guinea. (plos.org)
  • DNA transposons are very common in the Caenorhabditis elegans genome, as well as several relatively high-copy-number families of their nonautonomous relatives, miniature inverted-repeat transposable elements (MITEs). (asmscience.org)
  • In addition, we identified 80 candidate miRNAs that originated from transposable elements or repeats, especially miniature inverted-repeat elements (MITEs). (biomedcentral.com)
  • We have reason to believe that, in a genome, the founder sequences of different families of retroposons are in competition with regard to the amplification/fixation process. (springer.com)
  • Zietkiewicz E, Rafalski A, Labuda D (1994) Genome fingerprinting by simple sequence repeat (SSR)-anchored polymerase chain reaction amplification. (springer.com)
  • Transposable elements are classified into two major categories based on the specific steps of their amplification method. (bioscience.org)
  • Enzymatic amplification of beta-globin genomic sequences keywords forex credit restriction site analysis for diagnosis of sickle cell anemia. (retzepti.ru)
  • TANDEM REPEAT SEQUENCES are copies which lie adjacent to each other, direct or inverted (INVERTED REPEAT SEQUENCES). (umassmed.edu)
  • Repetitive elements comprise ~45% of the human genome and consist of interspersed repeats derived from non-autonomous or autonomous transposable elements and tandem repeats of simple sequences (satellite DNA) or complex sequences. (blog-biosyn.com)
  • Sat2 sequences are composed of variants of two tandem repeats of ATTCCATTCG followed by one or two copies of ATG. (blog-biosyn.com)
  • Tandem repeats finder: a program to analyze DNA sequences. (geneticsmr.com)
  • The evaluation of the genomic sequence led to the identification of more than one hundred artifactual tandem duplications that were eliminated by re-assembling the genome. (pubmedcentralcanada.ca)
  • 5S rDNA has long been a favored target for cytological and phylogenetic studies due to the inherent peculiarities of its structural organization, such as the tandem arrays of repetitive units and their high interspecific divergence. (biomedcentral.com)
  • The Tc1/mariner Family of Transposable Elements, p 519-532. (asmscience.org)
  • We have used a transient assay system to investigate the promoter region of the maize Suppressor-mutator (Spm) transposable element. (syr.edu)
  • Raina, R , Cook, D & Fedoroff, N 1993, ' Maize Spm transposable element has an enhancer-insensitive promoter ', Proceedings of the National Academy of Sciences of the United States of America , vol. 90, no. 13, pp. 6355-6359. (syr.edu)
  • In this study, we measured the nuclear DNA content of Vallisneria spinulosa by flow cytometry, performed a de novo assembly, and annotated repetitive sequences by using a combination of next-generation sequencing (NGS) and bioinformatics tools. (peerj.com)
  • Most importantly, this software must be easy to use, as many of today's plant genome sequencing groups have only limited bioinformatics expertise and computational resources. (plantphysiol.org)
  • As the rough draft of the human genome sequence nears a finished product and other genome-sequencing projects accumulate sequence data exponentially, bioinformatics is emerging as an important tool for studies of transposon biology. (beds.ac.uk)
  • Bridged nucleic acids ( BNA3 ) are artificial bicyclic oligonucleotides that contain a six-membered bridged structure with a "fixed" C 3 '-endo sugar puckering. (blog-biosyn.com)
  • Single-stranded RNA (ssRNA) transcripts from transposons and repetitive regions of the genome are thought to be generated by Pol IV activity (Pikaard et al. (weebly.com)
  • Transposons are composed by DNA and rolling-circle (RC) elements and mobilize through a DNA intermediate, while retrotransposons are composed by Long Terminal Repeats (LTR) and non-LTR (LINE and SINE) sequences that take advantage of an mRNA intermediate for their mobilization [ 1 , 2 ]. (biomedcentral.com)
  • The unique interpretation about accelerated evolution and the novel idea that the transposable elements such as LINEs and DNA transposons are involved in maintaining the host genome besides its own transposition natures were proposed. (elsevier.com)
  • Transposable elements are found abundantly in non-coding DNA and the Alu family of SINE transposons accounts for approximately 10% of the total DNA in the human genome ( Cordaux & Batzer, 2009 ). (peerj.com)
  • Tc1/mariner transposons are widespread DNA transposable elements (TEs) that have made important contributions to the evolution of host genomic complexity in metazoans. (biomedcentral.com)
  • Most mariner-type elements are known only from their sequences obtained through homology-based PCR screens or by sequence analysis (genomic or expressed sequence tag). (asmscience.org)
  • At first considered to represent different families, Tc1 , mariner , and IS630 were later gathered together as the IS630/Tc1/mariner (ITm) group, based on their shared mode of transposition via a DNA intermediate, their TA target site, and transposase sequence homology [ 8 , 9 ]. (biomedcentral.com)
  • Copy number variation of this repeat most likely accounts for the polymorphism in the mouse pseudoautosomal region detected with a probe from the flanking sequences. (biomedsearch.com)
  • Standard methods for detecting repetitive sequence are therefore probably missing large numbers of transposable element fragments. (pubmedcentralcanada.ca)
  • Sequencing of these fragments should expose the presence of unusual features typical of pseudogenes, unless the nuclear integration is very recent and has not yet been mutated. (biomedcentral.com)
  • Comparative analysis of the repetitive DNA distribution and organization in the wild beet and in the addition lines allowed the development of a physical model of the chromosomal fragments. (hindawi.com)
  • Here, plant genome organization was addressed by means of cloning and sequencing TE fragments of different types, which compose the largest portion of the Aegilops speltoides genome. (hindawi.com)
  • A significant number of clones consisted of intercalated fragments of TEs of various types, in which Fatima (Ty3- gypsy ) sequences predominated. (hindawi.com)
  • Transposable elements (TEs) are fragments of DNA that can move to new genomic locations. (pnas.org)
  • Also note these fragments represent the end of the repeat, as there is no unaligned consensus sequence following the last fragment. (ucsc.edu)
  • In cases where there is unaligned consensus sequence between the fragments, the repeat will look like the following. (ucsc.edu)
  • The dotted line indicates the length of the unaligned sequence between the two fragments. (ucsc.edu)
  • In all vertebrate lineages, there is evidence of transposable element-mediated genomic rearrangements such as insertions, deletions, inversions and duplications potentially associated with or subsequent to speciation events. (springer.com)
  • Our data provide evidence for an "accordion" model of genome size evolution in birds and mammals, whereby the amount of DNA gained by transposable element expansion, which greatly varies across lineages, was counteracted by DNA loss through large segmental deletions. (pnas.org)
  • Kalb VF, Glasser S, King D, Lingrel JB (1983) A cluster of repetitive elements within a 700 base pair region in the mouse genome. (springer.com)
  • Our study is concerned with a fundamental question about the human genome sequence: what is it made of? (pubmedcentralcanada.ca)
  • MultiPipMaker and supporting tools: Alignments and analysis of multiple genomic DNA sequences. (repeatmasker.org)
  • We mined the non-redundant database of NCBI using BLASTp searches, with transposase sequences from a diverse set of reference Tc1/mariner elements as queries. (biomedcentral.com)
  • Through multiple-alignment of transposase sequences from a diverse collection of previously identified and recently annotated elements from a wide range of organisms, we identified the putative DDE/D triad for all superfamilies. (pnas.org)
  • Sequence and comparative analysis of the chicken genome provide unique perspectives on vertebrate evolution. (repeatmasker.org)
  • Genome sequence of the Brown Norway rat yields insights into mammalian evolution. (repeatmasker.org)
  • Transposable elements (TEs) have significantly influenced the evolution of transcriptional regulatory networks in the human genome. (biomedcentral.com)
  • Britten RJ, Baron WF, Stout DB, Davidson EH (1988) Sources and evolution of human Alu repeated sequences. (springer.com)
  • Dynamic and Evolution of Transposable Elements. (geneticsmr.com)
  • These two regions differ in the organization of both 5S rDNA and the neighboring sequences comprised of transposable elements, implying different modes of evolution for these regions. (biomedcentral.com)
  • Initial sequencing and comparative analysis of the mouse genome. (repeatmasker.org)
  • A new method of analyzing phylogenetic relations among members of sequence family (Quentin 1988) discriminates at least six possible B1 subfamilies in the mouse genome. (springer.com)
  • Krayev AS, Markusheva TV, Kramerov DA, Ryskov AP, Skryabin KG, Bayev AA, Georgiev GP (1982) Ubiquitous transposon-like repeats B1 and B2 of the mouse genome: B2 sequencing. (springer.com)
  • Transposable elements (TEs) make up at least half of the human genome [ 1 , 2 ], however, the vast majority of the approximately 3.5 million TE insertions are fixed, ancient repeats. (biomedcentral.com)
  • Editor: John M. Greally, Albert Einstein College of Here, using a PCR-based targeted bulk sequencing approach, we profiled 9,181 somatic Medicine, UNITED STATES insertions from 20 postmortem tissues from five Rett patients and their matched healthy Received: August 15, 2018 controls. (deepdyve.com)
  • insertions contribute to genomic diversity and MeCP2 dysfunction alters their genomic pat- Data Availability Statement: Sequencing data are terns in Rett patients. (deepdyve.com)
  • The first region contained highly diverged short-type 5S rDNA units that were disrupted by multiple insertions of transposable elements. (biomedcentral.com)
  • Also, our study established a basis for further biochemical and molecular biological studies for understanding roles of the repetitive sequence in the subterminal region in transposition. (genetics.org)
  • To provide broader insights into the molecular basis of the pathogenicity-associated traits of the basal Mucorales, we report the full genome sequence of L. corymbifera and compared it to the genome of Rhizopus oryzae , the most common cause of mucormycosis worldwide. (plos.org)
  • It was first discovered in Ascobolus immersus and is required for the de novo methylation of cytosine in repeated sequences during meiosis. (biomedcentral.com)
  • Methylation interference studies demonstrate adjacent minor and major groove contacts at the inner part of the binding site by the N-terminal 68 amino acids of the DNA binding domain. (vu.nl)
  • Alu sequences located upstream of the CDKN2A promoter were found to be hypermethylated in cancer cell lines, and an Alu sequence located in intron 6 of TP53 showed extensive methylation in normal and cancer cells. (blog-biosyn.com)
  • Higgins DG, Gouy M (1987) Interfacing similarity search software with the sequence retrieval system ACNUC. (springer.com)
  • The structural similarity to native nucleic acids and the presence of a nitrogen atom within the bicyclic ring leads to very good solubility in water and allows for easy handling of synthetic primers and probes. (blog-biosyn.com)
  • We find strong collinearity of the flanking regions among haplotypes on each side of the S-locus together with high levels of sequence similarity. (prolekarniky.cz)
  • Tc1/mariner , hAT , P ) primarily on the basis of sequence similarity of the transposase. (pnas.org)
  • The transforming sequences lie within the coding region for a M(r) 61,000 protein, but the fragment itself does not appear to specify a viral polypeptide. (elsevier.com)
  • A total of 4,130 putative unannotated protein-coding sequences were identified in the 20% of reads which mapped in intergenic regions. (biomedcentral.com)
  • For most eukaryotic organisms, protein coding sequences are only a small portion of the genome. (oatd.org)
  • Possibly it is the way of reconstructing Sleeping Beauty transposase that is responsible for generating a protein that is more active than any element found in nature, where it is not in the best interest of the parasite transposable element to encode a transposase that is too active and might kill the host. (asmscience.org)
  • The transposases from several superfamilies possess a protein domain containing an acidic amino acid triad (DDE or DDD) that catalyzes the "cut and paste" transposition reaction. (pnas.org)
  • Further, alignment coverage peaks on specific positions of the TE consensus sequences, illuminating a diversity of TE-specific RBP binding motifs. (biomedcentral.com)
  • Furthermore, we identified additional highly conserved amino acid residues or motifs within the DDE/D domain that together form a "signature string" that is specific to each superfamily. (pnas.org)
  • Sequence comparisons of the six LTRs indicate that there is conservation of sequences derived from the 5' terminus of viral RNA and extensive divergence of the 3'-specific sequences. (nih.gov)
  • In the wild, ongoing chromosomal rearrangements lead to considerable changes in the numbers, sizes, and positions of highly repetitive DNA clusters and underlie the divergence of natural populations [ 21 ]. (hindawi.com)
  • Nucleotide sequence analysis of the long terminal repeat (LTR) of avian retroviruses: structural similarities with transposable elements. (nih.gov)
  • Analysis of the nucleotide sequence of the LTR from one clone, lambda RAV2-2, reveals several putative regulatory sites for the initiation and termination of transcription. (nih.gov)
  • The basis of this specificity has been investigated by DNA sequence analysis of the sites where 18 P elements are found. (nih.gov)
  • We then used these TE sequences to carry out a genome-wide analysis of C to T mutations biases. (biomedcentral.com)
  • Nevertheless, due to their repetitive nature it is considerably hard to integrate TE analysis into genome-wide studies. (inria.fr)
  • Gouy M, Milleret F, Mugnier C, Jacobzone M, Gautier C (1984) ACNUC: a nucleic acid sequence data base and analysis system. (springer.com)
  • Gouy M, Gautier C, Milleret F (1985) System analysis and nucleic acid sequence banks. (springer.com)
  • Mannella CA, Frank J, Delihas N (1987) Interrelatedness of 5S RNA sequences investigated by correspondence analysis. (springer.com)
  • Genome sequence analysis elucidates many of the novel aspects of leptospiral physiology relating to energy metabolism, oxygen tolerance, two-component signal transduction systems, and mechanisms of pathogenesis. (asm.org)
  • Single copy sequences suitable for use as DNA probes can be defined by computational analysis of genomic sequences. (patentsencyclopedia.com)
  • In spite of having such a general role and expected frequent occurrence genome wide, there is no DNA sequence analysis based tool to identify boundary elements. (omictools.com)
  • Our study provides an overview of Tc1-mariner phylogeny and summarises the impressive diversity of Tc1-mariner TEs among sequenced eukaryotes. (biomedcentral.com)
  • Thus, to date, Tol2 is the only active autonomous transposable element found in a vertebrate genome. (genetics.org)
  • The majority of the repetitive sequences are LTR-retrotransposons comprising 43% of the genome. (peerj.com)
  • Repetitive DNA-specifically, transposable elements (TEs)-constitutes at least 45% of the human genome, wherein the fraction of long interspersed nucleotide element (LINE) retrotransposons is 17% [ 1 ]. (hindawi.com)
  • It is not yet known whether the low density of repetitive DNA elements in the chicken is due to low transposable element activity or to a lack of active retrotransposons in the chicken genome. (beds.ac.uk)
  • LTR retrotransposons are predominant, representing 50.7% of the total nucleotide sequence. (beds.ac.uk)
  • The complete DNA sequences of the 2.9 kb element and four small elements (previously isolated from hybrid-dysgenesis-induced mutations of the white locus) have been determined. (nih.gov)
  • A revertant of one of the white locus mutants has been found to result from precise excision of the P element, restoring the wild-type DNA sequence. (nih.gov)
  • The organization of 5S rDNA into repetitive clusters and their NTS variation have made them a popular tool for cytological and phylogenetic studies. (biomedcentral.com)
  • At the chromosomal level, different TE clones demonstrated sequence-specific patterning, emphasizing the effect of the TE fraction on the Ae . (hindawi.com)
  • Citation Query Role of transposable elements in heterochromatin and epigenetic control. (psu.edu)
  • Role of transposable elements in heterochromatin and epigenetic control. (psu.edu)
  • Approximately one half of the human genome consists of repetitive sequences or 'repeats' which are generally packaged in heterochromatin. (umn.edu)
  • Constitutive heterochromatin in centromeric and peri-centromeric regions also becomes relatively more open, and the transcription of satellite sequences increases. (wiley.com)
  • Mobster uses discordant read pairs and clipped reads in combination with consensus sequences of known active mobile elements. (biomedcentral.com)
  • Our approach is able to generate high-quality consensus TE sequences automatically, requiring the user to only provide a few basic parameters. (biomedcentral.com)
  • We also found other, presumably paralogous, solo-LTRs in a consensus sequence of the underlying Copia -like transposable element. (biomedcentral.com)
  • Dotted lines above the repeat and extending left or right indicate the length of unaligned repeat consensus sequence. (ucsc.edu)
  • Only the 5' proximal fragment of the consensus sequence is aligned to the genome. (ucsc.edu)
  • TERMINAL REPEAT SEQUENCES flank both ends of another sequence, for example, the long terminal repeats (LTRs) on RETROVIRUSES. (umassmed.edu)
  • P[hswa] carries white-apricot (wa) sequences, including a complete copia element, under the control of an hsp70 promoter, and resembles the original wa allele in eye color phenotype. (umd.edu)
  • To determine whether the formation of multimers is a common feature of MITEs, we performed a more thorough survey, including an estimation of the proportion of multimers, with 30.2 Mb of publicly available rice genome sequence. (plantcell.org)
  • Transposable elements or repeats, especially MITEs, are rich sources for miRNA origination. (biomedcentral.com)