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)
Most other SINEs are derived from tRNAs including the MIRs (mammalian-wide interspersed repeats). (lookformedical.com)
Many polymorphisms are located in the estimated 98% ofthe human genome that does not encode protein.This experiment examines a polymorphism in the human genome that iscaused by the insertion of an Alu transposon, or transposable element.Alu is a member of the family of short interspersed elements (SINEs) andis approximately 300 nucleotides in length. (e-dokumen.com)
Repetitive short interspersed elements (SINEs) are retrotransposons ubiquitous in mammalian genomes and are highly informative markers to identify species and phylogenetic associations. (biomedcentral.com)
Repetitive short interspersed elements (SINEs) are ubiquitous eukaryotic retrotransposons. (biomedcentral.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)
Both LINEs and SINEs elements, despite the differences in structure and transposition mechanisms ( [44] ), are ubiquitous components of eukaryotic genomes, playing a major role in their evolution. (sisef.it)
There are 250000 copies of LINE elements in Lilium ( [21] ) and SINEs are represented, for example, by 50000 copies in tobacco ( [46] ). (sisef.it)
Long and Short Interspersed Elements (LINES and SINES) account for 21% and 13% of the genome, respectively. (cilecenter.org)
SINEs (Short Interspersed Nuclear Elements) are densest in housekeeping regions, for instance, where they modulate a host of genomic activities. (stferdinandiii.com)
Repeats7
Long terminal repeats (LTRs) similar to those from retroviruses are contained in retrotransposons and retrovirus-like elements. (lookformedical.com)
For example, one copy of a specific short tandem repeat (STR) region might have 10 repeats, while the other copy might have 11 repeats. (ojp.gov)
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)
Frameshifting events happening in short operates of pyrimidines (primarily C residues) in the repeats bring about mutations which might provide a system for escape of the LF3 function from sponsor surveillance. (molecularcircuit.com)
Their proteins items however have got different sequences and antibodies to 1 usually do not cross-react using the various other (28 29 Although EBV IRs resemble in proportions the brief interspersed elements within eukaryotic genomes whereas brief interspersed elements are usually noncoding and will become retrotransposons there is absolutely no proof for retrotransposition from the EBV tandem repeats. (molecularcircuit.com)
non-etheless like chromosomal recurring elements generally (21) by providing the chance of template-primer misalignments or era of template hairpin buildings during replication the viral repeats offer possibilities for replication infidelity or transcriptional variant and mutations. (molecularcircuit.com)
RepeatMasker - RepeatMasker is a program that screens DNA sequences for interspersed repeats and low complexity DNA sequences. (g6g-softwaredirectory.com)
Elements that are transcribed into RNA, reverse-transcribed into DNA and then inserted into a new site in the genome. (lookformedical.com)
Retrotransposable elements are important and peculiar genetic components derived from ancient retrovirus insertion inside plants genome. (sisef.it)
The analysis demonstrated the presence of multiple copies of retrotransposable elements inside the genome of beech, in accordance with the viral quasi-species theory of retrotransposon evolution. (sisef.it)
The identification of retrotransposable elements in forest trees represents an important step toward the understanding of mechanisms of genome evolution. (sisef.it)
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)
The observed differences in genome size in plants are accompanied by variations in the content of LTR retrotransposons, demonstrating that such elements might be important players in the evolution of plant genomes, along with polyploidy ( [11] ). (sisef.it)
These short RNAs participate in a diverse array of cellular processes including gene regulation, chromatin dynamics and genome defense. (biomedcentral.com)
As part of the genome sequencing initiative for the tammar, we have explored the evolution of each of the major classes of mammalian small RNAs in an Australian marsupial for the first time, including the first genome-scale analysis of the newest class of small RNAs, centromere repeat associated short interacting RNAs (crasiRNAs). (biomedcentral.com)
A type of primate-specific transposable element , or "jumping gene," that is roughly 300 base pairs long and exists in large copy number across all chromosomes of primate genomes (over 1 million copies in the human genome). (anthropogeny.org)
Amino acids are encoded by the genome as different three nucleotide codes. (anthropogeny.org)
Nucleotide sequence divergence in each TE copy was calculated as the Kimura distance between the annotated TE copies in the genome and the consensus sequence of each TE family C ultrametric timetree depicting the position of Tr. (pensoft.net)
Repetitive DNAelements account for approximately half of the genome and are normally highly methylated, thus the observed DNA demethylation may involve repetitive DNAelements. (biomedcentral.com)
Sequences6
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)
Nucleotide sequences, usually upstream, which are recognized by specific regulatory transcription factors, thereby causing gene response to various regulatory agents. (lookformedical.com)
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)
The degree of relatedness or homology between the sequences is predicted computationally or statistically based on weights assigned to the elements aligned between the sequences. (lookformedical.com)
The provided input sequences are scanned against selected genomes using the Bowtie algorithm, which is designed for efficient short sequence matching. (g6g-softwaredirectory.com)
PhyML - PhyML is a software product that estimates maximum likelihood phylogenies from alignments of nucleotide or amino acid sequences. (g6g-softwaredirectory.com)
Retroelements2
Class I elements (or RETROELEMENTS - such as retrotransposons, retroviruses, LONG INTERSPERSED NUCLEOTIDE ELEMENTS and SHORT INTERSPERSED NUCLEOTIDE ELEMENTS) transpose via reverse transcription of an RNA intermediate. (edu.au)
To investigate the expression of long interspersed element (LINE) 1, human endogenous retrovirus (HERV) K10, and short interspersed element-VNTR-Alu element (SVA) retrotransposons in ejaculated human spermatozoa by means of reverse-transcription (RT) polymerase chain reaction (PCR) analysis as well as the potential incorporation of cloned human and mouse active retroelements in human sperm cell genome. (nih.gov)
Retrotransposons4
Long interspersed nuclear element-1 (L1) retrotransposons are a source of divergent genetic information in hominoid genomes, but their importance in physiological functions and their contribution to human brain evolution are largely unknown. (lu.se)
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)
Genomes3
It is therefore clear that retrotransposable elements build large parts of eukaryotic genomes ( [40] ). (sisef.it)
Repetitive elements of an unknown function surprisingly account for the large fractions of our genomes. (cilecenter.org)
The genomes used have previously been processed using RepeatMasker to remove repetitive elements, that are Not similar to known miRNAs. (g6g-softwaredirectory.com)
Repetitive elements3
There are two classes of interspersed repetitive elements. (edu.au)
Three of these repetitive elements (called IR 1 IR 3 and TR respectively) are found in latent viral proteins EBV nuclear antigens 5 and 1 and LMP2A and -B (membrane proteins). (molecularcircuit.com)
The other two repetitive elements IR 2 (or and LF3 (leftward reading body 3) are located in the polyribosomal small fraction of EBV-infected cells and represent one of the most abundant viral transcripts synthesized through the EBV lytic routine (5 11 15 17 30 Their open up reading structures are almost completely PF-3644022 made up of the recurring elements. (molecularcircuit.com)
Genes5
The Dnmt3a and Dnmt3L genes are critical mediators of cytosine methylation during gametogenesis, with major actions noted at transposable elements and imprinted loci. (elsevierpure.com)
Transposition of this element into coding and regulatory regions of genes is responsible for many heritable diseases. (lookformedical.com)
Genes of IAP elements (a family of retrovirus-like genetic elements) which code for virus-like particles (IAPs) found regularly in rodent early embryos. (ouhsc.edu)
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)
All three TashAT genes are located together in a tight cluster, interspersed by two further small open reading frames, all facing head to tail. (lookformedical.com)
Nuclear elements2
LINEs (Long Interspersed Nuclear Elements) are by contrast a common feature of tissue-specific chromosome domains, where they commonly act as chromosome "scaffold attachment regions" that determine how strands of DNA will fold and unfold in the nucleus. (stferdinandiii.com)
7- 9 All reported mutations are single nucleotide alterations leading to splice site, missense, nonsense, or frameshift mutations, or intra-exonic deletions and insertions of up to four nucleotides, which have been detected through exonic PCR amplifications and sequencing. (bmj.com)
In total, KoVariome includes 12.7M single-nucleotide variants (SNVs), 1.7M short insertions and deletions (indels), 4K structural variations (SVs), and 3.6K copy number variations (CNVs). (nature.com)
Such mechanisms business lead both to nucleotide deletions and insertions of G residues in paramyxoviruses (4 16 or in bovine parainfluenza pathogen 3 towards the expression of most three reading structures in its P gene (32). (molecularcircuit.com)
Nucleic acid1
The sequential correspondence of nucleotides in one nucleic acid molecule with those of another nucleic acid molecule. (lookformedical.com)
Transposable element1
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)
Sequence5
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)
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)
Commonly observed BASE SEQUENCE or nucleotide structural components which can be represented by a CONSENSUS SEQUENCE or a SEQUENCE LOGO. (lookformedical.com)
A sequence of amino acids in a polypeptide or of nucleotides in DNA or RNA that is similar across multiple species. (lookformedical.com)
Humans2
SVA elements are~2-kb hominid-specific noncoding RNAs that have resulted in single-gene disease in humans through insertional mutagenesis or aberrant mRNA splicing. (elsevierpure.com)
Exaptation of an ancient Alu short interspersed element provides a highly conserved vitamin D-mediated innate immune response in humans and primates. (oregonstate.edu)
SNPs1
The International HapMap project resolved human haplotypes into more than one million common single nucleotide polymorphisms (SNPs) in an effort to catalogue genetic variations associated with diseases 3 . (nature.com)
Long6
The long interspersed element 1 (LINE-1 or L1) ORF2 protein is the genomic source for RT activity required for mobilization of its own RNA in cis and other RNAs, such as SINE/variable-number tandem-repeat (VNTR)/Alu (SVA) elements, in trans. (elsevierpure.com)
It is normally 110 bp long, but in affected KBTs it contains a short interspersed nucleotide element (SINE) insertion. (omia.org)
We detected high levels of BNT162b2 in Huh7 cells and changes in gene expression of long interspersed nuclear element-1 (LINE-1), which is an endogenous reverse transcriptase. (freedomontario26.ca)
non-LTR and LTR elements characterized, respectively, by the absence or presence of long repeated regions flanking the ORFs core. (sisef.it)
The hypomethylation of long interspersed nucleotide element-1 (LINE-1) in colorectal carcinoma has been associated with genomic instability. (biomedcentral.com)
They lack the ability to copy and paste themselves directly, but are able to "hitchhike" via the activity of Long Interspersed Elements (LINEs) that have retained the ability to copy and paste. (anthropogeny.org)
Genomic1
Alu elements were considered to be a part of what has been called "junk DNA" because they do not code for the production of proteins, however they may serve some yet unknown function and definitely contribute to genomic plasticity, evolution, and disease. (anthropogeny.org)
Methylation2
We looked for RFLP/ Hpa II polymorphism in the Bov-A2 element in bovine Zebu breeds by PCR-RFLP, and examined whether polymorphism in this element is associated with methylation. (geneticsmr.com)
Quantitative analysis of repetitive element methylation was performed with a methylation-sensitive restriction followed by a quantitative PCR analysis (qPCR). (biomedcentral.com)
Copies1
the gypsy LTR element is present in 20000 copies in maize. (sisef.it)
Initiation2
In contrast to the abundance mutations in SDHB and SDHD , only a single multiply affected family and an isolated case, containing a single nucleotide initiation codon and a splice site mutations in SDHC , respectively, have been described by Niemann et al . (bmj.com)
This transcription initiation-factor structural module preorganizes template-strand ssDNA to engage the RNAP active center, thereby facilitating binding of initiating nucleotides and enabling transcription initiation from initiating mononucleotides. (osti.gov)
Polymorphism1
Furthermore, the high polymorphism of retrotransposable elements can represent a starting point for the development of new genetic variability markers. (sisef.it)
The promoter region of bovine CYP21 contains a short interspersed nucleotide element of Bov-A2, which overlaps a putative Sp1 binding site. (geneticsmr.com)
These transcripts are almost evenly divided between those arising from enhancer-associated (elncRNA) or promoter-associated (plncRNA) elements. (biomedcentral.com)
Single1
Equations describing renaturation Let C = concentration of single-stranded DNA at time t (expressed as moles of nucleotides per liter). (slidetodoc.com)
Classes1
Using next generation sequencing, we have characterized the major classes of small RNAs, micro (mi) RNAs, piwi interacting (pi) RNAs, and the centromere repeat associated short interacting (crasi) RNAs in the tammar. (biomedcentral.com)
Human1
For example, the evolutionary distance between chicken and human provides high specificity in detecting functional elements, both non-coding and coding. (cshl.edu)