GenomesRepeatsRetrotransposonsGenesTransposable elementsNuclearElementsWhole Exome SequencingSpeciesGeneIlluminaShortNucleotide sequencesInsertionsTranscriptionEukaryotesAnnotateNucleotidesGenomicsLongLineage-specificPhylogeneticAmplificationProteinsAmino acidPolymeraseCopiesLINEsLatimeriaGenomic sequenceUpstreamTransposonsQPCRHumanHighlyRepeatMaskerComplexityComparativeGenome wideLociRegulationSimilarityAnalysis
Genomes19
- Short interspersed elements (SINEs) are repetitive DNA sequences invading the genomes of eukaryotes. (eimb.ru)
- 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)
- Transposable elements, such as Long INterspersed Elements (LINEs), are DNA sequences that can replicate within genomes. (bvsalud.org)
- Repetitive short interspersed elements (SINEs) are retrotransposons ubiquitous in mammalian genomes and are highly informative markers to identify species and phylogenetic associations. (biomedcentral.com)
- For the analysis of unknown genomes, GenXPro employs a hybrid sequencing strategy, combining long PacBio reads with Illumina reads to produce the best possible and accurate assemblies at the lowest costs. (genxpro.net)
- We offer whole genome sequencing at different coverages for the genome wide detection of mutations and the analysis of copy-number variations (CNVs) in human and other genomes. (genxpro.net)
- Wide distribution of short interspersed elements among eukaryotic genomes. (medecinesciences.org)
- Sequence data now flow copiously, creating the challenges of understanding the information that our genomes contain, and applying the data and analysis to improve human welfare. (cilecenter.org)
- Sequencing genomes of other species facilitates and extends these goals by revealing general principles of biology. (cilecenter.org)
- Repetitive elements of an unknown function surprisingly account for the large fractions of our genomes. (cilecenter.org)
- The initial phase of genomics aims to map and sequence an initial set of entire genomes. (slidetodoc.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)
- Over the last few years next generation sequencing technologies (NGS) have revolutionized the fields of genomics and transcriptomics, providing the opportunity to analyze genomes and transcriptomes with high sequencing depth in a relatively short time in comparison with Sanger sequencing. (biomedcentral.com)
- Both LINEs and SINEs elements, despite the differences in structure and transposition mechanisms ( [44] ), are ubiquitous components of eukaryotic genomes, playing a major role in their evolution. (sisef.it)
- 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)
- Comparative evolutionary analysis of whole genomes requires not only accurate annotation of gene space, but also proper annotation of the repetitive fraction which is often the largest component of most if not all genomes larger than 50 kb in size. (biomedcentral.com)
- Repetitive elements contribute a large part of eukaryotic genomes. (biomedcentral.com)
- For example, about 40 to 50% of human, mouse and rat genomes are repetitive. (biomedcentral.com)
- Completion of eukaryotic genome sequencing projects is a difficult task, due to the large size of the genomes and the abundance of repeats in the genomes. (biomedcentral.com)
Repeats11
- Repetitive elements such as Simple Sequence Repeats (SSRs), Long and Short Interspersed Nuclear Elements (LINES und SINES), long terminal repeats (LTRs) as well as mitochondrial and other plastids-DNA will be covered, while the rest of the genome remains largely uncovered. (genxpro.net)
- 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)
- Clustered repeated sequences Human chromosomes, ideograms G-bands Tandem repeats on every chromosome: Telomeres Centromeres 5 clusters of repeated r. (slidetodoc.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)
- The use of repeat libraries of one species to detect repeats from a related species (that diverged e.g. 10 million years ago) is highly problematic as it is known that intergenic space is rapidly evolving for the high turnover rates of transposable elements and repetitive sequence. (biomedcentral.com)
- Conversely, de novo methods such as Piler [ 3 ] and RepeatModeler ( http://www.repeatmasker.org/RepeatModeler.html ) have been developed to identify repeats in genome assemblies based on the number of times a sequence motif appears in an input file. (biomedcentral.com)
- This track was created by using Arian Smit's RepeatMasker program, which screens DNA sequences for interspersed repeats and low complexity DNA sequences. (wustl.edu)
- 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). (wustl.edu)
- The function of repetitive elements has been discussed for a long time [ 3 ] and only recently has the importance of repeats in cellular processes begun to open up [ 4 ]. (biomedcentral.com)
- Alphoid repeats or human alpha satellites are a human specific subclass of satellite DNA, which are long sequences of non-coding DNA appearing in tandems, i.e. the repeat instances follow each other without long gaps. (biomedcentral.com)
Retrotransposons7
- 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)
- Repetitive short interspersed elements (SINEs) are ubiquitous eukaryotic retrotransposons. (biomedcentral.com)
- Retrotransposons are fragments of cDNA which are transcribed from RNA and then inserted in a permissive sequence of the genome ( splicesosomal introns , for instance, are permissive regions). (bredagenetics.com)
- Two retrotransposons, belonging to the two major classes of LTR and non-LTR elements, were characterized trough a SCAR (Sequence Characterized Amplified Region) strategy. (sisef.it)
- The cloning and sequencing of amplification products and a Cleaved Amplified Polymorphisms (CAPs) approach on the identified retrotransposons, showed a high level of diversity among the multiple copies of both elements. (sisef.it)
- Non-LTR retrotransposons can be divided in several subclasses, such as LINE (Long INterspersed Elements) and SINE (Short INterspersed Elements - [44] ). (sisef.it)
- In turn, these can be divided into long terminal repeat (LTR) retrotransposons, which refer to endogenous retroviruses (ERVs), and non-LTR retrotransposons, which include long interspersed element class 1 (LINE-1 or L1) and short interspersed elements (SINEs). (bioconductor.org)
Genes14
- Genes are categorized into families based on shared nucleotide or protein sequences. (wikipedia.org)
- Gene paralogs are genes with similar sequences from within the same species while gene orthologs are genes with similar sequences in different species. (wikipedia.org)
- Due to the similarity of their sequences and their overlapping functions, individual genes in the family often share regulatory control elements. (wikipedia.org)
- The genes are diverse in sequence and function displaying various levels of expression and separate regulation controls. (wikipedia.org)
- While these genomic parasites can be deleterious to the cell, the long-term being in the genome has made SINEs a valuable factor of genetic variation providing regulatory elements for gene expression, alternative splice sites, polyadenylation signals, and even functional RNA genes. (eimb.ru)
- have analyzed the tef-1α sequences of F. equiseti , as well as the toxin-related genes PKS13 , PKS4, and TRI5 [26], and Kari has successfully cloned a protease gene [27]. (researchsquare.com)
- Sequences of DNA in the genes that are located between the EXONS. (lookformedical.com)
- While our genes are encoded by a varying sequence of nucleotides, the genotype is determined by the DNA sequence, both nuclear and mitochondrial. (cilecenter.org)
- Know (close to) all the genes in a genome, and the sequence of the proteins they encode. (slidetodoc.com)
- To identify genes with an altered DNA methylation pattern during HSC activation, a genome-wide DNA methylation analysis was performed (EpiQuest Sequencing, Zymo Research). (biomedcentral.com)
- Sequence and organization of coelacanth neurohypophysial hormone genes: evolutionary history of the vertebrate neurohypophysial hormone gene locus. (xenbase.org)
- We have sequenced a coelacanth (Latimeria menadoensis) BAC clone encompassing the neurohypophysial hormone genes and investigated the evolutionary history of the vertebrate neurohypophysial hormone gene locus within a comparative genomics framework. (xenbase.org)
- Nucleotide sequences of the second exons of the two genes are under purifying selection implying a regulatory function. (xenbase.org)
- Comparison of nucleotide and deduced amino acid sequences of coelacanth vasotocin and mesotocin genes. (xenbase.org)
Transposable elements7
- There are several types: INTERSPERSED REPETITIVE SEQUENCES are copies of transposable elements (DNA TRANSPOSABLE ELEMENTS or RETROELEMENTS) dispersed throughout the genome. (lookformedical.com)
- 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 (TEs) are ancient (retro)-virus insertions inside a host genome and are peculiar mobile genetic elements accounting for a large proportion of repetitive DNA regions ( [29] ). (sisef.it)
- Here we present the Rice TE database (RiTE-db) - a genus-wide collection of transposable elements and repeated sequences across 11 diploid species of the genus Oryza and the closely-related out-group Leersia perrieri . (biomedcentral.com)
- In addition to the annotation of gene space, a detailed annotation of repeated sequences and transposable elements (TEs) ( e.g. presence/absence, types, and location) is critical for understanding the biology of a genome, as well as an important tool for the improvement of high-quality genome assemblies. (biomedcentral.com)
- Illumina): highly repetitive sequences and transposable elements pose significant problems to assembly algorithms. (biomedcentral.com)
- A conserved function of piRNAs across all bilateral animals is to silence sequence-complementary transposable elements (TEs) 1 , 2 , 3 , 4 . (gokcumenlab.org)
Nuclear4
- This generates a vast repertoire of transcripts that includes protein-coding messenger RNAs, long non-coding RNAs (lncRNAs) and repetitive sequences, such as SINEs (short interspersed nuclear elements). (nature.com)
- SINEs are "non-autonomous" such that amplification and integration is dependent on enzymes derived from the host genome and long interspersed nuclear elements (LINEs) [ 5 ]. (biomedcentral.com)
- First analysis of identifier elements, which belong to the class of short interspersed nuclear elements (SINE), showed a decrease of DNA methylation during HSC culture. (biomedcentral.com)
- However, treating Trp53 mutant MEF's with DNA demethylating agent caused a huge increase in the level of transcripts encoding short interspersed nuclear elements and other species of noncoding RNAs that generated a strong type 1 IFN response. (codondex.com)
Elements17
- Most cancers exhibit reduced methylation of repetitive sequences such as Long INterspersed Element-1 (LINE-1) and Alu elements. (biomedcentral.com)
- The repetitive elements can hereafter be used for comparative genomics approaches. (genxpro.net)
- The primate Alu (ALU ELEMENTS) and the rodent B1 SINEs are derived from 7SL RNA, the RNA component of the signal recognition particle. (lookformedical.com)
- Okada N. SINEs: short interspersed repeated elements of the eukaryotic genome. (medecinesciences.org)
- Nikaido M, Rooney AP, Okada N. Phylogenetic relationships among cetartiodactyls based on insertions of short and long interspersed elements: hippopotamuses are the closest extant relatives of whales. (medecinesciences.org)
- Long and Short Interspersed Elements (LINES and SINES) account for 21% and 13% of the genome, respectively. (cilecenter.org)
- Repetitive DNA elements account for approximately half of the genome and are normally highly methylated, thus the observed DNA demethylation may involve repetitive DNA elements. (biomedcentral.com)
- Additional repetitive DNA elements such as Line1 will be analyzed, to determine their contribution to DNA demethylation. (biomedcentral.com)
- There are 250000 copies of LINE elements in Lilium ( [21] ) and SINEs are represented, for example, by 50000 copies in tobacco ( [46] ). (sisef.it)
- A hallmark of cancer, autoimmunity and disease is the aberrant transcription of typically silenced, repetitive genetic elements that mimic Pathogen-Associated Molecular Patterns (PAMP's) that bind Pattern Recognition Receptors (PPR's) triggering the innate immune system and inflammation. (codondex.com)
- Jurka J. Repbase update: a database and an electronic journal of repetitive elements . (wustl.edu)
- Recently, Li (Bioinformatics 35:4408-4410, 2019) developed a novel software tool dna-brnn to annotate repetitive sequences using a recurrent neural network trained on sample annotations of repetitive elements. (biomedcentral.com)
- This combines the basic concepts of Li (Bioinformatics 35:4408-4410, 2019) with current techniques developed for neural machine translation, the attention mechanism, for the task of nucleotide-level annotation of repetitive elements. (biomedcentral.com)
- A recent overview of functions and the evolution of repetitive elements can be found in [ 9 ]. (biomedcentral.com)
- While [ 11 ] mainly describes structural properties of two of the four repetitive element classes, we additionally highlight the biological importance and, if possible, function of specific repetitive elements. (biomedcentral.com)
- DNA transposons are natural genetic elements residing in the genome as repetitive sequences. (biomedcentral.com)
- Vertical bars represent repetitive elements (LINE, LF-SINE, LmeSINE1 and AmnSINE1). (xenbase.org)
Whole Exome Sequencing1
- With whole exome sequencing (WES), all exon coding regions of the human genome are sequenced. (genxpro.net)
Species4
- We find SINEs are powerful markers of speciation and conclude that the few inconsistencies with expected patterns of speciation likely represent incomplete lineage sorting, species hybridization and SINE-mediated genome rearrangement. (biomedcentral.com)
- SINE insertions as clade markers for wild crucifer species. (medecinesciences.org)
- False negatives arise due to repeat/TE sequence diversification across taxa which can hamper the identification of distinctive repeat features ( i.e. lineage specific sequences) of the species. (biomedcentral.com)
- This annotation step is traditionally performed using alignment based methods, either in a de novo approach or by aligning the genome sequence to a species specific set of repetitive sequences. (biomedcentral.com)
Gene10
- Knowing the sequence of the protein encoded by a gene can allow researchers to apply methods that find similarities among protein sequences that provide more information than similarities or differences among DNA sequences. (wikipedia.org)
- Gene families are highly variable in size, sequence diversity, and arrangement. (wikipedia.org)
- Multigene families typically consist of members with similar sequences and functions, though a high degree of divergence (at the sequence and/or functional level) does not lead to the removal of a gene from a gene family. (wikipedia.org)
- In some instances, gene members have identical (or nearly identical) sequences. (wikipedia.org)
- Some gene families also contain pseudogenes, sequences of DNA that closely resemble established gene sequences but are non-functional. (wikipedia.org)
- SINE sequences are approximately 70-700 base pairs (bp) averaging about 250 bp [ 1 ] with most organized into an RNA gene-derived region, a di-nucleotide repeat region and terminating in a poly A or poly A/T tail [ 2 - 4 ]. (biomedcentral.com)
- Direct phenotypic variation is possible by altering gene expression via insertion into coding regions or interference from the internal RNA polymerase promoters in SINEs [ 29 ]. (biomedcentral.com)
- Sequence homology is an indication of the genetic relatedness of different organisms and gene function. (lookformedical.com)
- Nucleotide sequences, usually upstream, which are recognized by specific regulatory transcription factors, thereby causing gene response to various regulatory agents. (lookformedical.com)
- To further test the effects of transposon-aided gene amplifications on genome evolution and architecture, the repetitive fraction of the significantly expanded genome of the banana pathogen, Pseudocercospora fijiensis , was analyzed in greater detail. (biomedcentral.com)
Illumina2
- In this study, the Illumina HiSeq 4000 and PacBio platforms were used to sequence and assemble the whole genome of Fusarium equiseti D25-1. (researchsquare.com)
- The deep RNA sequencing performed with Illumina technologies generated 145,435,156 paired-end reads, accounting for ~14 GB of sequence data, which were de novo assembled using a Trinity/CLC combined strategy. (biomedcentral.com)
Short1
- Furthermore, Alu represents the most abundant Short INterspersed Element (SINE) repetitive sequence, representing 11% of total human genome [ 26 ]. (biomedcentral.com)
Nucleotide sequences2
- 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)
- While most pachytene piRNAs lack obvious targets, neither the copy numbers nor nucleotide sequences of pachytene piRNA loci are conserved 5 , 6 , 7 , and many of them are not found in syntenic regions even in closely related mammals 8 , 9 . (gokcumenlab.org)
Insertions2
- Shedlock AM, Okada N. SINE insertions: powerful tools for molecular systematics. (medecinesciences.org)
- Transposons insertions usually generate repetitive units . (bredagenetics.com)
Transcription3
- Analysis of the dog genome revealed SINE insertion polymorphisms resulting in anti-sense transcription that provide alternate splice site junctions [ 30 ]. (biomedcentral.com)
- The region of DNA which borders the 3' end of a transcription unit and where a variety of regulatory sequences are located. (lookformedical.com)
- Using whole-genome sequencing of OS, we found features of TP53 intron 1 rearrangements suggesting a unique mechanism correlated with transcription. (oncotarget.com)
Eukaryotes1
- In eukaryotes, repetitive DNA sequences are transcriptionally silenced through histone H3 lysine 9 trimethylation (H3K9me3). (bvsalud.org)
Annotate1
- The fastest and most common way to annotate the repetitive fraction of a genome assembly is to create repeat libraries derived from a set of previously identified representative repetitive sequences and screen the target genome using homology-based searches. (biomedcentral.com)
Nucleotides1
- CpG-rich DNA fragments were concentrated, converted by bisulfite treatment and analyzed by next-generation sequencing to identify 5meC-modified nucleotides. (biomedcentral.com)
Genomics2
- Functional genomics aims to deduce information about the function of DNA sequences. (slidetodoc.com)
- Using long-insert jumping libraries at 105X mean physical coverage and linked-read whole-genome sequencing from 10X Genomics, we document seven major SV classes at ~5 kb SV resolution. (biomedcentral.com)
Long4
- The sequences are about 300 base pairs long and are repeated several thousand times throughout the genome. (ojp.gov)
- 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)
- Should continue long after the initial genome sequences have been completed. (slidetodoc.com)
Lineage-specific1
- The conserved molluscan biomineralization toolkit and lineage-specific repetitive low-complexity domains are essential to the construction of the nautilus shell. (nature.com)
Phylogenetic1
- Sequence analyses separated Feliform CanSINEs into two subfamilies, each characterized by distinct RNA polymerase binding motifs and phylogenetic associations. (biomedcentral.com)
Amplification1
- By applying different amplification regimes, hard-to-sequence genomic regions (e.g. (genxpro.net)
Proteins1
- Pachytene piRNAs have been proposed to either regulate mRNAs 10 , 11 , 12 , 13 , 14 or stabilize PIWI proteins for a function that does not require piRNA-guided sequence specificity 15 . (gokcumenlab.org)
Amino acid1
- Comparison of amino acid sequences of (A) vasopressin and (B) oxytocin family hormone precursors in vertebrates. (xenbase.org)
Polymerase1
- Highly repeated sequences, 6K-8K base pairs in length, which contain RNA polymerase II promoters. (lookformedical.com)
Copies4
- The Alu sequence family (named for the restriction endonuclease cleavage enzyme Alu I) is the most highly repeated interspersed repeat element in humans (over a million copies). (lookformedical.com)
- Sequences of DNA or RNA that occur in multiple copies. (lookformedical.com)
- TANDEM REPEAT SEQUENCES are copies which lie adjacent to each other, direct or inverted (INVERTED REPEAT SEQUENCES). (lookformedical.com)
- Even more-highly repeated sequences - minisatellites, microsatellites and telomeres - may appear as tens or even hundreds of thousands of copies, in aggregate amounting to 15% of the genome. (cilecenter.org)
LINEs1
- Okada N, Hamada M, Ogiwara I, Ohshima K. SINEs and LINEs share common 3' sequences: a review. (medecinesciences.org)
Latimeria1
- The comparison with the recently sequenced genome of the African congener Latimeria chalumnae and with the available genomic resources of other vertebrates revealed a good reconstruction of full length transcripts and a high coverage of the predicted full coelacanth transcriptome. (biomedcentral.com)
Genomic sequence1
- In this study, the complete genomic sequence of Fusarium equiseti D25-1 was determined using multiple sequencing platforms. (researchsquare.com)
Upstream1
- The splicing factor 3b/3a complex binds pre-mRNA upstream of the intron's branch site in a sequence independent manner and may anchor the U2 snRNP to the pre-mRNA. (cancer-genetics.org)
Transposons1
- LINE (also known as LINE-1 or L1 ), SINE and LTR transposons . (bredagenetics.com)
QPCR1
- Quantitative analysis of repetitive element methylation was performed with a methylation-sensitive restriction followed by a quantitative PCR analysis (qPCR). (biomedcentral.com)
Human4
- International Human Genome Sequencing Consortium. (medecinesciences.org)
- Initial sequencing and analysis of the human genome. (medecinesciences.org)
- Alu repetitions (which occur every 3 kb in the human genome) are SINE with an internal promoter . (bredagenetics.com)
- Performing genome-wide target profiling on data sets obtained by retrieving chromosomal targeting sequences from individual clones, we have identified several piggyBac and Tol2 hotspots and observed that (4) piggyBac and Tol2 display a clear difference in targeting preferences in the human genome. (biomedcentral.com)
Highly1
- a procedure to detect highly repetitive and transcribable sequences with tRNA-like structures. (medecinesciences.org)
RepeatMasker1
- RepeatMasker cannot know if an arbitrary sequence you give it is a SINE or a LINE or anything else. (stackexchange.com)
Complexity2
- This is very low sequence complexity, 2 letters or 20 bp. (slidetodoc.com)
- Time required for half-renaturation is directly proportional to sequence complexity (4) For a renaturation measurement, one usually shears DNA to a constant fragment length L (e. g. 400 bp). (slidetodoc.com)
Comparative1
- 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)
Genome wide1
- We sequenced 689 participants with autism spectrum disorder (ASD) and other developmental abnormalities to construct a genome-wide map of large SV. (biomedcentral.com)
Loci2
- However, mammalian piRNA sequences and piRNA-producing loci evolve more rapidly than the rest of the genome for unknown reasons. (gokcumenlab.org)
- Our results indicate that genetic instability at pachytene piRNA loci, while producing certain pathogenic SVs, also protects genome integrity against TE mobilization by driving the formation of rapid-evolving piRNA sequences. (gokcumenlab.org)
Regulation2
- Hastings, M. L., Ingle, H. A., Lazar, M. A. & Munroe, S. H. Post-transcriptional regulation of thyroid hormone receptor expression by cis-acting sequences and a naturally occurring antisense RNA. (nature.com)
- Transposases integrate DNA-Sequences preferentially into the genome regions that are nucleosome free and hence also accessible for transcriptional regulation. (genxpro.net)
Similarity1
- The database allows sequence browsing, downloading, and similarity searches. (biomedcentral.com)
Analysis2
- SINEBase is a database of SINEs and a toolset for their identification and analysis. (eimb.ru)
- 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)