Terminal repeat sequences. Medical search. Frequent questions

A transposon consists of several genes flanked by terminal repeat sequences. (i-sis.org.uk)
Comparisons of the available sequenced genomes suggest a minimum gene set for vascular plants of 4,223 genes. (biomedcentral.com)
Intriguingly, PePIF1 was transposed in the somaclonal variants of Phalaenopsis cultivars, as revealed by transposon display, and the newly inserted genes were identified and sequenced. (biomedcentral.com)
For his stunning discovery of the homology between acute transforming genes including the src gene, and its comparable sequence in normal cellular DNA which opened a new era of increasingly precise comprehension of cell differentiation, growth and development of living creatures, and of the molecular genetics of cancer, this 1982 Albert Lasker Basic Medical Research Award is given. (laskerfoundation.org)
Prediction of the coding sequences of unidentified human genes. (nih.gov)
To delete genes specifically from mammary gland, transgenic mice were created carrying the Cre gene under the control of the mouse mammary tumor virus (MMTV) long terminal repeat (LTR). (nih.gov)
TE sequences within the introns of human genes show an antisense orientation bias, which has been proposed to reflect selection against TE sequences in the sense orientation owing to their ability to terminate the transcription of host gene transcripts. (biomedcentral.com)
Using high-throughput sequencing data, we have characterized over 9,000 distinct TE-derived sequences that provide transcription termination sites for 5,747 human genes across eight different cell types. (biomedcentral.com)
TE sequences provide numerous termination sites to human genes, and TE-derived TTS are particularly cell type-specific. (biomedcentral.com)
There are several known examples whereby TE sequences located within, or nearby, human genes have been shown to terminate transcription of genic mRNAs. (biomedcentral.com)
There is also experimental evidence showing that L1 (LINE) retrotransposon sequences can terminate the transcription of human genes, and in this same study the intronic content of L1 sequences in human genes was found to be negatively correlated with their expression levels[ 9 ]. (biomedcentral.com)
Almost all reported CMS genes are chimeric structure, i.e., the exogenous sequence in the gene originated from nuclear DNA, chloroplast DNA, or mtDNA itself [ 19 ]. (biomedcentral.com)

Transposons are related to viruses and proviral sequences that, like transposons, are found in the genomes of all species. (i-sis.org.uk)
The experiment shows that the transposon can be stripped down to the bare minimum of the flanking repeats, and it can still jump into genomes. (i-sis.org.uk)
Thus, no full genome sequence of a gymnosperm species is available at present, whereas 30 angiosperm and more basal plant genomes have been sequenced. (nature.com)
However, size is not the only challenge to sequencing presented by conifer genomes. (nature.com)
The availability of conifer genome sequences would enable comparative analyses of genome architecture and the evolution of key traits for seed plants, including flower or fruit development and life history (perennial versus annual), and help to determine how and why conifer genomes became so large. (nature.com)
Viral metagenomic studies routinely uncover sequences with no recognizable homology to known coding regions or genomes. (peerj.com)
Rather, viral genomes are identified through an iterative approach, first omitting non-viral sequences. (peerj.com)
In contrast to eukaryotic and prokaryotic organisms, only a small fraction of viral genomes has been sequenced and characterized. (peerj.com)
Many lentiviral vector genomes used for gene therapy are derived from HIV-1 and contain sequences required for genome expression, encapsidation and reverse transcription. (researchsquare.com)
Oxford Nanopore sequencing showed that deleting 507 nt of env decreased the number of pre-mRNA splicing events per transcript and increased the proportion of unspliced genomes. (researchsquare.com)
Overall, this allows the creation of lentiviral vector genomes that contain minimal HIV-1 sequence, which could improve biosafety and increase the transgene capacity. (researchsquare.com)

16. The 5' regulatory sequences of active miR-146a promoters are hypomethylated and associated with euchromatic histone modification marks in B lymphoid cells. (nih.gov)
TEs contain their own regulatory sequences, including specific signals that lead to the termination of transcripts initiated from element promoters. (biomedcentral.com)

Retrieve, view, and download retroviral genomic and protein sequences. (nih.gov)
Galaxy based workflow system for MGEScan which is identifying long terminal repeats (LTR) and non-LTR retroelements in eukaryotic genomic sequences. (readthedocs.org)

These LTRs contain enhancer and promoter sequences for transcription. (jove.com)
The Delta element of Ty retrotransposons and LTRs (long terminal repeats) are examples of this concept. (nih.gov)
Long terminal repeats (LTRs) similar to those from retroviruses are contained in retrotransposons and retrovirus-like elements. (lookformedical.com)

The tool works with standard single letter nucleotide or protein codes including ambiguities and can match Prosite patterns in protein sequences. (nih.gov)
Nucleotide variations from the consensus sequence were observed in most isolates and clustered phylogenetically, corresponding to the geographic distribution of donor cattle. (nih.gov)
The present invention further provides nucleic acids comprising nucleotide sequences that encode mutant capsid proteins, and host cells comprising the nucleic acids. (justia.com)
Nucleotide sequences repeated on both the 5' and 3' ends of a sequence under consideration. (nih.gov)
Enough haplotypes clearly demonstrated the uniform structural characteristics of the B- atp6-orfH79 as follows: except for the conserved sequence (671 bp) composed of B- atp6 (619 bp) and the downstream followed the B- atp6 (52 bp, DS), and GSV sequence, a rich variable sequence (VS, 176 bp) lies between the DS and GSV with five insertion or deletion and more than 30 single nucleotide polymorphism. (biomedcentral.com)
Seven existed single nucleotide polymorphism in GSV section can be translated into eleven various amino acid sequences. (biomedcentral.com)

Variation in coding sequences of BLV structural proteins has been studied extensively, but little work has been done on sequence variability of non-coding regions, mostly located in LTR. (nih.gov)
Most of these sequences are uncharacterized and were not identified as related to cytoskeletal proteins. (bioone.org)
The PUM repeat with the N- and C-terminal regions pack together to form a right-handed superhelix that approximates a half doughnut structurally similar to the Armadillo (ARM) repeat proteins, beta-catenin and karyopherin alpha. (embl-heidelberg.de)
Two previously undetected domains were identified in a variety of RNA-binding proteins, particularly RNA-modifying enzymes, using methods for sequence profile analysis. (embl-heidelberg.de)
It contains a 19-bp terminal inverted repeat flanked by a 3-bp target site duplication and two coding regions encoding ORF1- and transposase-like proteins. (biomedcentral.com)
The complete sequences of 100 new cDNA clones from brain which code for large proteins in vitro. (nih.gov)
Thus, NMD serves as a 'cellular vacuum cleaner' that protects the cell from the potentially harmful effects of truncated proteins by eliminating mRNAs with PTCs in a sequence of events that is not yet fully understood. (biomedcentral.com)

17. The role of human endogenous retroviral long terminal repeat sequences in human cancer (Review). (nih.gov)
We have shown that the abnormal X-Y interchange occurred between retroviral long terminal repeats (LTR). (bmj.com)
Human endogenous retroviral elements (HERVs), for example, have polyadenylation signals in their long terminal repeat (LTR) regions that terminate transcription[ 6 ]. (biomedcentral.com)

The BLV transcriptional promoter is located in the proviral 5' long terminal repeat (LTR), composed of U3, R, and U5 regions. (nih.gov)
Consistent with the known dependence of long terminal repeat (LTR) retrotransposons on tRNA primers, we demonstrate that LTR retrotransposons are, in fact, preferentially de-repressed in Asterix mutants. (nih.gov)
The Long terminal repeat (LTR) is about 600 nt long, of which the U3 region is 450, the R sequence 100 and the U5 region some 70 nt long. (wikipedia.org)
The piggyBac is 2.5kb long with 13 bp inverted terminal repeats. (i-sis.org.uk)
LOCUS AF029671 164 bp DNA PLN 16-NOV-1997 DEFINITION Chlamydomonas reinhardtii transposon Tcr1 left long terminal repeat, complete sequence. (bio.net)
LOCUS AF029672 164 bp DNA PLN 16-NOV-1997 DEFINITION Chlamydomonas reinhardtii transposon Tcr1 right long terminal repeat, complete sequence. (bio.net)
There are two types of retrotransposons - Long terminal repeat, or LTR, retrotransposons, and non-LTR retrotransposons - both of which use different transposition mechanisms. (jove.com)
The LTR retrotransposons consist of a 5-7kb long protein-coding region flanked at both ends by long terminal repeats, typically 250-600 bp in length. (jove.com)
LTR retrotransposons are class I transposable elements with long terminal repeats flanking an internal coding region. (jove.com)
A sequence within the U5 region of the 5' long terminal repeat (LTR) has previously been described as exerting posttranscriptional repression. (open.ac.uk)
Instead, the large genome size seems to result from the slow and steady accumulation of a diverse set of long-terminal repeat transposable elements, possibly owing to the lack of an efficient elimination mechanism. (nature.com)
The N-terminal region has been predicted to fold into a beta-propeller domain composed of seven beta-sheets each about 60 amino acid residues long, with the I-domain inserted between beta-sheets 2 and 3. (embl.de)
In a long and particularly close scientific collaboration with Dr. Varmus, Dr. Bishop showed beyond question that a DNA sequence in the avian sarcoma virus was virtually identical to a sequence in normal human DNA. (laskerfoundation.org)
Dr. Hanafusa's studies and those of others discovered that when retroviruses reproduce, they give rise to a DNA copy of themselves known as a "provirus" with identical gene-activating "long terminal repeat" sequences at either end. (laskerfoundation.org)
Cre-recombinase under the control of mouse mammary tumor virus long terminal repeat (MMTV) was expressed in the salivary gland and mammary epithelial cells of adult mice, and induced recombination in all tissues. (nih.gov)
Store the lyophilized protein at -80 °C. Lyophilized protein remains stable until the expiry date when stored at -80 °C. Aliquot reconstituted protein to avoid repeated freezing/thawing cycles and store at -80 °C for long term storage. (biovendor.com)
TDP43 (aka TARDBP) was originally identified as a protein which binds to the transactivation response (TAR) sequence found in the long terminal repeat of the HIV-1 virus genome. (biolegend.com)
mCMV/hEF1-HTLV prom: This composite promoter combines mouse cytomegalovirus (mCMV) immediate-early gene 1 enhancer, the elongation Factor-1α (EF-1α) core promoter, as well as the R segment and part of the U5 sequence (R-U5') of the Human T-Cell Leukemia Virus (HTLV) type 1 long terminal repeat. (invivogen.com)
More intriguing is the discovery of several new classes of NMD targets, including mRNAs that use translational +1 frameshifting, bicistronic mRNAs and, most interestingly, two classes of noncoding RNAs: pseudogene transcripts and transcripts encoded by transposable elements or their long terminal repeat (LTR) sequences. (biomedcentral.com)

The eight repeats and the N- and C-terminal regions form the Pumilio homology domain (PUM-HD). (embl-heidelberg.de)
Regardless of the environment explored, the overwhelming majority of viral sequences produced exhibit no sequence homology to characterized viral species. (peerj.com)
The fourfold repeated domain of OSF-2 shows homology with the insect protein fasciclin Periostin mRNA is expressed in the developing mouse embryonic and fetal heart, and that it is localized to the endocardial cushions that ultimately divide the primitive heart tube into a four-chambered heart. (biovendor.com)
Combined with the high-homology sequences in GenBank, a total of eighteen haplotypes have been revealed, only with ten haplotypes in orfH79 and its variants (GSV) that belong to three species (i.e. (biomedcentral.com)

BLV LTR contains multiple cis-acting elements important for promoter activity, a short coding sequence (encoding the NH(2) terminus of the G4 regulatory protein), and non-regulatory/non-coding regions. (nih.gov)
The binding of Rex protein to a sequence at the 3' end of viral mRNA, known as the Rex response element (RxRE) leads to removal of posttranscriptional repression. (open.ac.uk)
Amino acid sequence of mouse nidogen, a multidomain basement membrane protein with binding activity for laminin, collagen IV and cells. (embl.de)
The encoded protein contains an N-terminal leucine-rich repeat domain and a C-terminal coiled-coil domain. (nih.gov)
An evolutionarily conserved leucine-rich repeat protein CLERC is a centrosomal protein required for spindle pole integrity. (nih.gov)
FIG. 6 provides amino acid sequences corresponding to amino acids 570-610 of AAV2 ( FIG. 5 ) of AAV capsid protein VP1 of various AAV serotypes. (justia.com)

This element is characterized by 11-bp terminal inverted repeats and putative TTAA targets site duplications. (girinst.org)
Some repeats contain putative calcium-binding sites. (embl.de)
Furthermore, two distinct families, PePIF1a and PePIF1b , with 29 and 37 putative autonomous elements, respectively, were isolated, along with more than 3000 non-autonomous and miniature inverted-repeat transposable element (MITE)-like elements. (biomedcentral.com)

10 11 In general, XX maleness is the result of the transfer of the testis determining factor ( SRY ) to the X chromosome 12 as a result of an abnormal X-Y interchange involving the non-recombining region of Yp and homologous sequences in Xp. (bmj.com)
The 7-fold repeat domain is homologous to a similar domain in phosphatidylinositol-glycan-specific phospholipase D. (embl.de)
In close scientific collaboration, Dr. Varmus and Dr. J. Michael Bishop showed unequivocally that a genetic sequence in the avian sarcoma virus was homologous to a sequence in the normal DNA of vertebrates, including man. (laskerfoundation.org)

several bioinformatic solutions have been created to aid in detecting viral sequences within mixed communities (e.g. (peerj.com)
To determine the functional relevance of the viral sequences in the vector genome, we performed a deletion analysis. (researchsquare.com)

Comparative sequencing of Pinus sylvestris , Abies sibirica , Juniperus communis , Taxus baccata and Gnetum gnemon reveals that the transposable element diversity is shared among extant conifers. (nature.com)

The CpG island in the promoter of Dnajb1 and two contraoriented ERV class II repeats in Glcci1 were validated to display underlying stochasticity in methylation patterns common to metastable epialleles. (nih.gov)

LOOPERN5_DR copies are ~12% divergent from the consensus sequence. (girinst.org)
The C-terminal domain (CTD) of RPB1 contains tandem heptapeptide repeats with the consensus sequence YSPTSPS. (thermofisher.com)

It has a specificity for sites with the base sequence TTAA. (i-sis.org.uk)

Pumilio family members are characterised by the presence of eight tandem copies of an imperfectly repeated 36 amino acids sequence motif, the Pumilio repeat, surrounded by a short N- and C-terminal conserved region. (embl-heidelberg.de)

Find regions of similarity between this sequence and other sequences using BLAST. (nih.gov)
Among them, a potential autonomous element was identified by similarity analysis against the whole-genome sequence of Phalaenopsis equestris and named PePIF1 . (biomedcentral.com)

Transposable elements (TEs) encode sequences necessary for their own transposition, including signals required for the termination of transcription. (biomedcentral.com)

Assembled contigs were polished with Illumina paired-end data and connected and ordered using mate-pair libraries sequenced on both Illumina and SOLiD platforms, followed by further scaffolding and gap filling with 30× coverage of PacBio reads longer than 6,000 bp. (nature.com)
We sequenced the genome of the sacred lotus variety 'China Antique' with 94.2 Gb (101×) Illumina and 4.8 Gb (5.2×) 454 sequences. (biomedcentral.com)

Importance of cleaning cycle sequencing reactions In the sanger sequencing workflow, cycle sequencing reaction is certainly the core and critical step because the reaction determines if the extension products are appropriately synthesized and labeled with great. (advancedseq.com)

The whole amino acid sequence of nidogen was deduced from cDNA clones isolated from expression libraries and confirmed to approximately 50% by Edman degradation of peptides. (embl.de)

Note that the sequence of available ORFs provided by InvivoGen can differ from a given reference Genbank record due to genetic variations and/or alternative splicing. (invivogen.com)

The data support a previously proposed dumb-bell model of nidogen by demonstrating a large N-terminal globular domain (641 residues), five EGF-like repeats constituting the rod-like domain (248 residues) and a smaller C-terminal globule (328 residues). (embl.de)
The segment C-terminal to the beta-propeller domain, residues 599-1092, was studied with nine mAbs. (embl.de)

Two more EGF-like repeats interrupt the N-terminal and terminate the C-terminal sequences. (embl.de)
While there is evidence in support of this model for some elements, the extent to which TE sequences actually terminate transcription of human gene across the genome remains an open question. (biomedcentral.com)
TE-TTS were much more likely to be found in the sense orientation than other intragenic TE sequences of the same TE family and TE-TTS in the sense orientation terminate transcription more efficiently than those found in the antisense orientation. (biomedcentral.com)
An early study of HERVs provided the first direct evidence that TE-derived sequences can terminate the transcription of non-TE human mRNAs and further suggested that different subfamilies of these elements may serve to terminate transcription in a cell type-specific manner[ 7 ]. (biomedcentral.com)

Nidogen contains two consensus sequences for tyrosine sulfation and for asparagine beta-hydroxylation, two N-linked carbohydrate acceptor sites and, within one of the EGF-like repeats an Arg-Gly-Asp sequence. (embl.de)

Finds sub-sequences or patterns in the sequence and highlights the matching regions. (nih.gov)
Weak sequence homologies (25%) were detected between some regions of nidogen, the LDL receptor, thyroglobulin and the EGF precursor. (embl.de)

Phosphorylation and other modifications within this sequence influence the recruitment of factors that regulate the transcription cycle. (thermofisher.com)
Finally, combining the deletion in gag with moving the RRE downstream of the 3' R to prevent its reverse transcription showed that substantial amounts of HIV-1 sequence can be removed from the vector genome without compromising transduction efficiency. (researchsquare.com)
βGlo pAn: The human beta-globin 3'UTR and polyadenylation sequence allow the efficient arrest of the transgene transcription. (invivogen.com)

Using whole genome bisulphite sequencing of DNA from the livers of five mice from the A vy colony, we searched for sites at which DNA methylation differed among the mice. (researchgate.net)

By comparing the sequence now known at the "src" gene, as it occurs in the DNA of various species, Dr. Varmus and Dr. Bishop showed that the gene is conserved from species to species with other minor changes, indicating that its role must be important. (laskerfoundation.org)

PCR product cleaning before Sanger sequencing PCR products are the most common template for Sanger sequencing to confirm the right sequence or detect a single or a few mutations. (advancedseq.com)

Here, we report the sequencing and analysis of the sacred lotus genome, which descends from the most ancient lineage of angiosperms. (biomedcentral.com)
During capillary electrophoresis, a particular type of polymer is injected into capillary array and used as liquid separation matrix for Sanger sequencing or fragment analysis. (advancedseq.com)
Capillary array as a carrier for polymers, the separation media, is critical for peak separation in Sanger sequencing and fragment analysis. (advancedseq.com)

We constructed a hybrid nuclear genome assembly starting from 9× sequence coverage with Roche 454 technology. (nature.com)

LOCUS CEITS1 624 bp DNA PLN 19-NOV-1997 DEFINITION Chlamydomonas eugametos internal transcribed spacer 1, complete sequence. (bio.net)
LOCUS CPITITS1 519 bp DNA PLN 19-NOV-1997 DEFINITION Chlamydomonas pitschmannii internal transcribed spacer 1, complete sequence. (bio.net)
LOCUS CPITITS2 525 bp DNA PLN 19-NOV-1997 DEFINITION Chlamydomonas pitschmannii internal transcribed spacer 2, complete sequence. (bio.net)
and internal transcribed spacer 2, complete sequence. (bio.net)

Evidence for birch gene models was obtained by sequencing EST libraries from 12 different birch tissues or growth conditions, providing 18,951 transcripts with an average length of 1,683 bp, and by carrying out de novo assembly of RNA-seq reads, yielding 16,906 transcripts ( Supplementary Figs. 7 and 8 , Supplementary Tables 3 and 4 , and Supplementary Note ). (nature.com)

Design and test primers for this sequence using Primer-BLAST. (nih.gov)

Metagenomics has enabled sequencing of viral communities from a myriad of different environments. (peerj.com)

The transmembrane subunit of the BLV envelope glycoprotein, gp30, contains three completely conserved YXXL sequences that fit an endocytic sorting motif. (mdpi.com)

The local chromatin environment for these TE-TTS is similar to that seen for 3 ′ UTR canonical TTS and distinct from the chromatin environment of other intragenic TE sequences. (biomedcentral.com)
For any individual human, different kinds of somatic cells contain the same genome sequence, but are obviously functionally distinct. (biomedcentral.com)

We have recently updated the text corpora to tokens, or sequences of tokens, and extensively we use in our research with respect to these criteria. (nih.gov)

The positive element is shown to be present within the 3' terminal 312 bp of the MLV psi + and to remove R ex-dependency by activating the nucleocytoplasmic transport of psi 312-containing mRNAs. (open.ac.uk)

Here we sequenced 150 birch individuals and assembled a B. pendula reference genome from a fourth-generation inbred line, resulting in a high-quality assembly of 435 Mb that was linked to chromosomes using a dense genetic map. (nature.com)
virMine automates sequence read quality control, assembly, and annotation. (peerj.com)

In contrast to other viral genome detection tools that often rely on the recognition of viral signature sequences, virMine is not restricted by the insufficient representation of viral diversity in public data repositories. (peerj.com)
Second, even when sequencing purified virions, sequencing data often includes non-viral (host) DNA. (peerj.com)

A simple introduction of CRISPR Clustered Regularly Interspaced Short Palindromic Repeat or CRISPR as a part of bacterial defense system against bacteriophage is used as a dominating gene-editing tool to make changes in targeted DNA sequences. (advancedseq.com)

These results show that pigeons prefer variable over fixed response sequences, and provide further support for the prediction of behavioral momentum theory (Nevin & Grace, 2000) that resistance to change and preference should be correlated. (abainternational.org)

LOCUS AB007370 1733 bp DNA PLN 03-OCT-1997 DEFINITION Chlamydomonas tetragama gene for 18S rRNA, partial sequence. (bio.net)

Human nidogen: complete amino acid sequence and structural domains deduced from cDNAs, and evidence for polymorphism of the gene. (embl.de)

The Cre recombinase from bacteriophage P1 excises intervening DNA sequences located between two unidirectional lox sites positioned on the same linear DNA segment, leaving one lox site behind. (nih.gov)

Pumilio-like repeats that bind RNA. (embl-heidelberg.de)
Class 2 inhibitors bind to the C-terminal heptad repeat (C-HR) of gp41. (nih.gov)

Anatomy18

Organisms39

Diseases10

Chemicals and Drugs62

Analytical, Diagnostic and Therapeutic Techniques and Equipment22

Phenomena and Processes123

Information Science4

Genes12

Genomes11

Regulatory sequences2

Genomic2

LTRs3

Nucleotide6

Proteins7

Retroviral3

Long19

Homology4

Protein6

Putative3

Homologous3

Viral sequences2

Transposable element1

Promoter1

Consensus sequence2

TTAA1

Amino acids1

Similarity2

Encode1

Illumina2

Workflow1

CDNA clones1

GenBank1

Residues2

Terminate4

Tyrosine1

Regions2

Transcription3

Methylation1

Species1

Mutations1

Analysis3

Genome assembly1

Complete sequence4

Libraries1

Primers1

Environments1

Motif1

Distinct2

Extensively1

MRNAs1

Assembly2

Data2

Bacterial1

Prediction1

RRNA1

Human1

SEGMENT1

Bind2