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Repetitive Sequences, Nucleic AcidShort Interspersed Nucleotide ElementsBase SequenceLong Interspersed Nucleotide ElementsMolecular Sequence DataAlu ElementsNucleic Acid RenaturationNucleic Acid HybridizationInterspersed Repetitive SequencesDNASequence Homology, Nucleic AcidDNA Transposable ElementsCloning, MolecularSequence Analysis, DNAGenome, PlantDNA, PlantRepetitive Sequences, Amino AcidDNA, SatelliteChromosome MappingChromosomes, Artificial, Bacterial3' Flanking RegionBlotting, SouthernCentromereDNA Restriction EnzymesEvolution, MolecularDendrobiumZoster Sine HerpeteGenomeTandem Repeat SequencesSpecies SpecificityAmino Acid SequencePhylogenySequence AlignmentPolymerase Chain ReactionGenomic LibraryPhysical Chromosome MappingPrimed In Situ LabelingGenesHeterochromatinRestriction MappingIn Situ Hybridization, FluorescenceChromosomes, PlantChromosome WalkingDNA ProbesChromosomesDeoxyribonuclease BamHIProtothecaCosmidsContig MappingNucleic Acid ConformationBase CompositionGene LibraryDNA, FungalDeoxyribonucleases, Type II Site-SpecificGenetic VariationTranscription, GeneticGenome, HumanDNA, RecombinantDNA MethylationOncorhynchus ketaDNA FingerprintingGenomic Structural VariationRecombination, GeneticDNA, BacterialPlasmidsIntronsModels, GeneticMultigene FamilyMicrosatellite RepeatsTelomereArtiodactylaRetroelementsDinucleotide RepeatsChromosomes, Artificial, YeastDNA PrimersCetaceaOryza sativaExonsConserved SequenceConsensus SequencePhysarumGenes, PlantRNABiological Evolution2-AcetylaminofluoreneDatabases, Nucleic AcidDNA, RibosomalGenetic MarkersChromosomes, FungalNucleic Acid DenaturationInverted Repeat SequencesRNA, TransferSequence Homology, Amino AcidChromosome BandingFrameshift MutationPrimatesGenomicsPolymorphism, Restriction Fragment LengthPolymorphism, GeneticDNA, Protozoan
GenomeTransposableGenomesRetrotransposonsRepeatsNucleotide sequenceGenesRegulatoryMaizeGeneElementsLongBaseEssentialSpecificSingleShort Interspersed ElementsArtificial chromosomeTransposable elementsGenBankTransposonsGenomicNCBIMutationsAbundantClonesPrimerHumanAnalysisCopyTypePresenceLibraryInitialHighDatabasesStructure
Genome12
  • Transposons: These are DNA sequences that can move and replicate in different parts of a cell's genome. (wikipedia.org)
  • There are several types: INTERSPERSED REPETITIVE SEQUENCES are copies of transposable elements (DNA TRANSPOSABLE ELEMENTS or RETROELEMENTS) dispersed throughout the genome. (lookformedical.com)
  • Previously, the genome of the cereal pathogen Fg was sequenced and shown to encode a larger number of proteins in pathogenicity related protein families compared to non-pathogenic fungi, including predicted transcription factors, hydrolytic enzymes, and transmembrane transporters 5 . (nature.com)
  • We sequenced Fv strain 7600 and Fol strain 4287 (Methods, Supplementary Table 1 ) using a whole-genome shotgun approach and assembled the sequence using Arachne ( Table 1 , ref. 6 ). (nature.com)
  • In this study, we sequenced the complete genome of Nautilus pompilius in the hope of providing a critical reference for the evolution of cephalopods. (nature.com)
  • We describe the establishment and analysis of a genus-wide comparative framework composed of 12 bacterial artificial chromosome fingerprint and end-sequenced physical maps representing the 10 genome types of Oryza aligned to the O. sativa ssp. (biomedcentral.com)
  • japonica reference genome sequence. (biomedcentral.com)
  • Our strategy is to develop bacterial artificial chromosome (BAC)-end sequence (BES) physical frameworks of the ten genome types of Oryza and align them to the reference sequence. (biomedcentral.com)
  • Introns sequences account for about 30% of the genome. (blogspot.com)
  • Like mammalian genomes, the sea urchin genome contains a lot of junk DNA, especially repetitive DNA. (blogspot.com)
  • By scanning the available genome sequences, Demuth et al. (blogspot.com)
  • Using whole-genome sequencing of OS, we found features of TP53 intron 1 rearrangements suggesting a unique mechanism correlated with transcription. (oncotarget.com)
Transposable6
  • Transposable elements, such as Long INterspersed Elements (LINEs), are DNA sequences that can replicate within genomes. (bvsalud.org)
  • Therefore, the opposite strand is sequenced discontinuously as both replication forks approach the center of the transposable element. (wikipedia.org)
  • 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. (lookformedical.com)
  • Transposable elements pervading mammalian genomes mostly originate from retrotransposons, including long interspersed nuclear elements (LINEs), short interspersed nuclear elements (SINEs), and endogenous retroviruses (ERVs) ( 2 , 3 ). (rna-mediated.com)
  • Here we report the construction of 12 BAC/BES framework physical maps derived from these libraries and an analysis of the BESs in terms of transposable element, simple sequence repeat (SSR), microRNA (miRNA), and single nucleotide variation (SNV) content. (biomedcentral.com)
  • Most of these sequences qualify as junk but they are littered with defective transposable elements that are already included in the calculation of junk DNA. (blogspot.com)
Genomes3
  • Long interspersed nuclear element-1 (L1) retrotransposons are a source of divergent genetic information in hominoid genomes, but their importance in physiological functions and their contribution to human brain evolution are largely unknown. (bvsalud.org)
  • a , Maximum-likelihood tree using concatenated protein sequences of 100 genes randomly selected from 4,694 Fusarium orthologous genes that have clear 1:1:1:1 correlation among the Fusarium genomes and have unique matches in Magnaporthe grisea , Neurospora crassa and Aspergillus nidulans . (nature.com)
  • Both genomes have been completely sequenced [ 17 , 18 ] and serve as the reference sequences for the major monocot and dicot plant lineages. (biomedcentral.com)
Retrotransposons1
  • Here we report that H3K9me3 is preferentially transferred onto the leading strands of replication forks, which occurs predominantly at long interspersed nuclear element (LINE) retrotransposons (also known as LINE-1s or L1s) that are theoretically transcribed in the head-on direction with replication fork movement. (bvsalud.org)
Repeats3
  • TERMINAL REPEAT SEQUENCES flank both ends of another sequence, for example, the long terminal repeats (LTRs) on RETROVIRUSES. (lookformedical.com)
  • Most other SINEs are derived from tRNAs including the MIRs (mammalian-wide interspersed repeats). (lookformedical.com)
  • Over 932 Mb of end sequence was analyzed for repeats, simple sequence repeats, miRNA and single nucleotide variations, providing the most extensive analysis of Oryza sequence to date. (biomedcentral.com)
Nucleotide sequence1
Genes2
Regulatory2
  • The region of DNA which borders the 3' end of a transcription unit and where a variety of regulatory sequences are located. (lookformedical.com)
  • Nucleotide sequences, usually upstream, which are recognized by specific regulatory transcription factors, thereby causing gene response to various regulatory agents. (lookformedical.com)
Maize1
  • We sequenced two additional Fusarium species, Fv , a maize pathogen that produces fumonisin mycotoxins that can contaminate grain, and F. oxysporum f.sp. (nature.com)
Gene1
  • Sequence homology is an indication of the genetic relatedness of different organisms and gene function. (lookformedical.com)
Elements1
Long2
  • Long-read RNA sequencing technologies, including Oxford Nanopore and PacBio, can directly sequence relatively long transcripts, thus providing the opportunity to examine full-length LINE transcripts. (bvsalud.org)
  • Highly repeated sequences, 100-300 bases long, which contain RNA polymerase III promoters. (lookformedical.com)
Base2
  • The 5 to 9 base pair overhang is left on either side of the target sequence allowing it to join to its target sequence in either orientation. (wikipedia.org)
  • The target molecule as a result contains the inserted element flanked by the 5 to 9 base pair sequences. (wikipedia.org)
Essential1
  • The conserved molluscan biomineralization toolkit and lineage-specific repetitive low-complexity domains are essential to the construction of the nautilus shell. (nature.com)
Specific1
  • 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. (lookformedical.com)
Single1
  • Simultaneously the donor strand is ligated to the target strand after cleavage leaving a single strand overhang on either end of the target sequence. (wikipedia.org)
Short Interspersed Elements2
  • Alu repetitive element is member of Short Interspersed Elements (SINE) in mammalian genome. (wikipedia.org)
  • The Alu repeat family comprises short interspersed elements (SINES) present in multiple copies in the genomes of humans and other primates. (nih.gov)
Artificial chromosome1
  • Bacterial Artificial Chromosome. (nih.gov)
Transposable elements1
  • 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)
GenBank4
  • An Accession number is a unique identifier given to a sequence when it is submitted to one of the DNA repositories ( GenBank , EMBL , DDBJ ). (nih.gov)
  • BankIt is a tool for the online submission of one or a few sequences into GenBank and is designed to make the submission process quick and easy. (nih.gov)
  • BankIt also automatically uses VecScreen to identify segments of nucleic acid sequence that may be of vector, adapter, or linker origin to combat the problem of vector contamination in GenBank . (nih.gov)
  • When new sequences are submitted to GenBank, the submission is checked for new organism names, which are then classified and added to the Taxonomy database. (nih.gov)
Transposons1
  • Typically considered "selfish" parasitic sequences, recent findings dispute this traditional model and have demonstrated the multifaceted potential of transposons. (biomedcentral.com)
Genomic6
  • The limitation of genomic survey sequence is that it lacks long-range continuity because of its fragmentary nature, which makes it harder to forecast gene and marker order. (wikipedia.org)
  • Single-pass sequencing with lower fidelity can be used on the rapid accumulation of genomic data but with a lower accuracy. (wikipedia.org)
  • This is despite the recent progress made in wheat genomic sequencing. (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)
  • Long Interspersed Element-1 (LINE-1 or L1) is the only active autonomous retrotransposon in humans and its activity is responsible for ~ 30% of genomic mass. (biomedcentral.com)
  • The Alu sequence is approximately 300 bp in length and is found commonly in intron s, 3′ untranslated regions of genes, and intergenic genomic regions. (nih.gov)
NCBI1
  • To add to the mix, in 1990 the NCBI and the NLM initiated a journal-scanning program to capture and annotate sequences reported in the literature that had not been submitted to any of the sequence databases. (nih.gov)
Mutations2
  • In this review, we propose that such noninherited bacterial DNA integration into chromosomes in human somatic cells could induce mutations leading to cancer or autoimmune diseases in a manner analogous to mobile elements and viral integrations. (prolekarniky.cz)
  • There is never "enough" sequencing 100 million species 7 billion individuals CS 273 a Lecture CS 273 a 2014 4, Autumn 08, Batzoglou Somatic mutations (e. g. (slidetodoc.com)
Abundant1
  • Almost 1 million copies of the Alu sequence are estimated to be present, making it the most abundant mobile element. (nih.gov)
Clones1
  • A larger insert is often helpful for the sequence project in organizing clones. (wikipedia.org)
Primer1
  • The Alu universal primer sequence is as follows: 5′-GTG GAT CAC CTG AGG TCA GGA GTT TC-3′ (26-mer). (nih.gov)
Human2
  • By using special Alu sequence as target locus, specific human DNA can be obtained from clone of TAC, BAC, PAC or human-mouse cell hybrid. (wikipedia.org)
  • While deep sequencing and qPCR analysis have shown that L1 copy number is much higher in certain parts of the human brain, direct in vivo studies regarding detection of L1-encoded proteins is lacking due to ineffective reagents. (biomedcentral.com)
Analysis1
  • Since fragment of DNA can be inserted into sequences, if an exon is inserted into intron, the transcript will be longer than usual and this transcript can be trapped by analysis. (wikipedia.org)
Copy1
  • These sequences act like very low copy plasmids that there is only one copy per cell sometimes. (wikipedia.org)
Type1
  • A. tumefaciens specifically transfers 10-30 kbp of DNA from its 200-800 kbp tumor-inducing (Ti) plasmid to plants via the bacterial type IV secretion system [1] . (prolekarniky.cz)
Presence1
  • The Alu sequence is so named because of the presence of a recognition site for the Alu I endonuclease in the middle of the Alu sequence. (nih.gov)
Library1
  • For the estimation of repetitive sequences, GSS plays an important role in the early assessment of a sequencing project since these data can affect the assessment of sequences coverage, library quality and the construction process. (wikipedia.org)
Initial1
  • The initial deposition of a sequence record is referred to as version 1. (nih.gov)
High1
  • 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)
Databases3
  • A sequence comparison algorithm that is optimized for speed and used to search sequence databases for optimal local alignments to a query. (nih.gov)
  • Furthermore, the protein sequence databases ( SWISS-PROT and PIR ) each developed their own taxonomic classifications that were very different from each other and from the nucleotide database taxonomies. (nih.gov)
  • The resulting hybrid was, at first, a bigger mess than any of the pieces had been, but it gave us a starting point that spanned all of the names in all of the sequence databases. (nih.gov)
Structure1
  • Inheritance, homology by common descent, and the conservation of sequence and structure in the determination of function are all central ideas in biology that are directly related to the evolutionary history of any group of organisms. (nih.gov)