Genomic 5 flanking region. Medical search. Frequent questions

These features are governed by a 2.2 kb differentially methylated domain, hereafter termed imprinting control region (ICR) in the 5'-flank of the H19 gene. (kb.se)
By means of laser-dissection and bisulfite genomic sequencing, it was observed that de novo methylation of CTCF target sites occurred in BORIS-expressing spermatocytes that exhibit repression of CTCF gene. (kb.se)
The coding region of the carboxy- terminal half of polyhedrin was removed and the remainder was ligated with the IGF II gene in phase to create a fusion protein gene consisting of the coding region of the amino-terminal half of polyhedrin and the IGF II gene. (microbiologyresearch.org)
This fusion protein gene was combined in a plasmid with the promoter and 5′ and 3′ flanking regions of the polyhedrin gene. (microbiologyresearch.org)
DEFINITION Mus musculus 129SVJ mNB-3 gene for neural recognition molecule NB-3, exon 1 and promoter region. (nig.ac.jp)
The gene encoding the Ov-phy-1 open reading frame contained 11 introns, similar in structure to the gene encoding human prolyl 4-hydroxylase isoform I. Genomic Southern blot, EST and genomic PCR studies demonstrated that the O. volvulus genome contained between three and eight genes closely related to Ov-phy-1. (embl.de)
We had isolated a PME gene from a tomato genomic library, including 2.59 kb of 5′ flanking region and the coding region. (ox.ac.uk)
Two introns of 106 and 1039 bp were found in the coding region and phylogenetic analysis placed this PME gene closer to genes from Citrus sinensis and Arabidopsis thaliana than tomato fruit-specific PME genes. (ox.ac.uk)
The complete gene for human fatty acid ethyl ester Synthase-III (FAEES-III) was isolated from a human genomic lambda phage library for functional and structural determination. (elsevierpure.com)
The gene spans approximately 3.3 kb which includes 791 base pairs of the 5' and 124 base pairs of the 3' flanking regions. (elsevierpure.com)
The gene for FAEES-III was localized to human chromosome 11 by hybridizing the genomic fragment Xh01 to Chinese hamster/human somatic cell hybrid panels. (elsevierpure.com)
BLAST-able datasets include Cucumis sativus genomic DNA, splice-aligned transcripts and proteins, gene models, and other aligned sequences. (plantgdb.org)
Targeted genomic editing using the CRISPR/Cas9 methodology has opened exciting new avenues in probing gene function in virtually any model system, including cultured mammalian cells. (biomedcentral.com)
Clonal screening for CRISPR/Cas9-mediated editing events using dot immunoblot is a straightforward and efficient approach that facilitates rapid generation of genomic mutants to study gene function. (biomedcentral.com)
Competition for PRPF8 availability alters the transcription-coupled splicing of RNAs in which weak 5′ splice sites predominate, enabling diversification of human gene expression during biological processes like mitosis. (biomedcentral.com)
DNA sequence analysis showed the patient's father was a heterozygote for the nonsense mutation of the ADAMTS13 gene (exon 21: c.G2651A: p.W884X), while the mother was a heterozygote for the non-synonymous mutation of the ADAMTS13 gene (exon 5: c.A530G: p.Y177C). (bvsalud.org)
We demonstrate that gene constructions that include the GAP-43 5'-flanking region along with sufficient sequences of the first intron drive beta-galactosidase (lacZ) expression to mimic in many regards the complex spatial and temporal pattern of endogenous GAP-43 expression. (harvard.edu)
Here, we report the isolation and analysis of 5' flanking genomic DNA regions upstream to the CAD gene, from two conifers, i.e. white spruce (Picea glauca (Moench) Voss) and loblolly pine (Pinus taeda L.). Sequence comparisons with available CAD gene promoters from angiosperms highlighted the conservation of cis-elements matching MYB, WRKY and bHLH binding sites. (ox.ac.uk)
Gene transcription is mainly regulated by transcription factors (TFs) that bind to specific DNA sequences (called motifs) located in the promoter regions of genes [ 1 ]. (biomedcentral.com)
To delimit the control elements that mediate tissue-specific and sex hormone-responsive apo[a] transcription, we derived a reporter YAC in which 40 kb of 5' flanking sequences from the cloned apo[a] allele were linked to a luciferase reporter gene. (zhihuiya.com)
To evaluate the origin of the detrimental mutation in the genes, parts of the 5' flanking regions were introduced into a Hep G2/simian virus 40 expression system with chloramphenicol acetyltransferase as a reporter gene, and transfected cells were analyzed for activity. (aspetjournals.org)
Ser amino acid substitution in a region that is a highly conserved in cytochromes P450 belonging to gene families 1 and 2. (aspetjournals.org)
To elucidate the molecular basis of the differential HCK gene expression, the genomic region containing the HCK promoter was isolated and functionally characterized. (uni-frankfurt.de)
Expression of a reporter gene linked to the −101HCK promoter region was up-regulated by Sp1, but not by other members of the Sp1 family of transcription factors, in Drosophila Schneider cells. (uni-frankfurt.de)
In 2004, a former graduate student, Julie Kerns, described the configuration of the dog ASIP gene based on a large genomic fragment cloned from a Doberman Pinscher (7). (springernature.com)

Several transcription regulatory sequences were identified in the promoter region. (elsevierpure.com)
This machinery recognizes pre-mRNA sequences at several motifs - the 5′ and 3′ splice sites, the branch point, and polypyrimidine tracts - positioned at exon-intron boundaries [ 4 ]. (biomedcentral.com)
Sequences of previously described binding sites were collected for these five factors present in the cis-regulatory regions of known target genes. (sdbonline.org)
Furthermore, an analysis of 4270 human genomic DNA and cDNA sequences has allowed us to confirm a correlation of GC 3 against GC 1+2 . (urosario.edu.co)
GAP-43 transgenic mice: dispersed genomic sequences confer a GAP-43-like expression pattern during development and regeneration. (harvard.edu)
At the time, we were more interested in protein-coding than regulatory sequences and only later did we realize that the region corresponding to the mouse HCP was deleted in the Doberman Pinscher DNA, an observation made by Chris Kaelin, a senior scientist in the lab (and owner of a chocolate and tan Dachshund). (springernature.com)
The group in Bern had a large collection of dog whole genome sequences, many with photographs that allowed Danika to think carefully about pattern phenotypes and their potential correlation with ASIP genomic variation. (springernature.com)
PROSITE is a method of determining what is the function of uncharacterized proteins translated from genomic or cDNA sequences. (open-bio.org)
In two of the transgenes studied, the cDNA of (hPC) was inserted at the translational start site of a 7.8 kbp mouse WAP genomic DNA Eco RI fragment containing 2.6 kbp of 5' flanking, 3.9 kbp WAP coding (exons and introns), and 1.3 kbp 3' untranslated region (UTR) and flanking sequences (designated WAPPC1 and WAPPC2). (vt.edu)
A third transgene consisted of only the 2.6 kbp of WAP 5' UTR and flanking DNA, 1.4 kbp hPC cDNA, and 1.3 kbp of 3' WAP UTR and flanking DNA with no linker sequences (designated WAPPC3). (vt.edu)

Search for any CsGDBgene or aligned sequence by ID or keyword , and download complete sequence or flanking 5' or 3' regions, exons, or introns (FASTA format). (plantgdb.org)
Preferentially retained introns and differentially used exons in the affected genes contain weak 5′ splice sites, but are otherwise indistinguishable from adjacent spliced introns. (biomedcentral.com)

Using transgenic mice, we have examined the expression pattern conferred by regions of genomic GAP-43 coupled to beta-galactosidase. (harvard.edu)
This genomic clone was used to generate transgenic mice. (zhihuiya.com)

This phenomenon, termed genomic imprinting, is highlighted by the neighboring Igf2 and H19 genes, which are monoallelically expressed on opposite parental chromosomes. (kb.se)
Analyzing 5′-upstream non-protein-encoding regions of the human mitochondrial function-associated genes, we speculate that mitochondrial functions could be recovered or improved at a transcriptional level. (intechopen.com)
Recent additions to the sequence database have also allowed separate analyses of the 5′ flanking regions of CpG island and non-CpG island genes as well as analyses of 3′ flanking regions, which suggest that the GC levels of 3′ flanking regions are closer to those of intergenic DNA than are those of other regions of genes. (urosario.edu.co)
In contrast, Hp1 and Dim5 mutants that are impacted in chromatin-associated processes upstream of DNA methylation are severely affected in development and virulence and display transcriptional reprogramming in specific hypervariable genomic regions (so-called adaptive genomic regions) that contain genes associated with host colonization. (biomedcentral.com)
In addition, mutations in the 5' flanking region common to both CYP2D6Ch genes were found. (aspetjournals.org)

A part of the upstream region of base pairs -1407 to -1068 was found to constitute an enhancer element, but the CYP2D6Ch-specific mutations did not influence the chloramphenicol acetyltransferase activity in the expression system. (aspetjournals.org)
A DNA fragment containing 101 base pairs of the 5′-flanking sequence showed strong promoter activity in the macrophage cell line RAW264 but was inactive in the non-monocytic cell lines HUT-78 and NIH-3T3. (uni-frankfurt.de)
Based on a previous GWAS study, 14 DA associated loci and flanking regions were selected for NGS (6,996,180 base pairs). (cdc.gov)

but only two of these, an Arg101Stop mutation in exon 2, and an Arg257Cys variation in exon 5, are known to have functional consequences. (aspetjournals.org)
One mutation was a non-synonymous mutation (exon 5: c.A530G: p.Y177C), while the other was a nonsense mutation (exon 21: c.G2651A: p.W884X). (bvsalud.org)

The DM2 repeat tract contains a flanking region 5' to the tract that consists of a polymorphic repetitive sequence (TG)14-25(TCTG)4-11(CCTG) n. (tmc.edu)
CAGG) repeat tract and the flanking sequence, as well as genetic selection assays may reveal the mechanisms responsible for the repeat instability in E. coli, and this may lead to a better understanding of the mechanisms contributing to the human disease state. (tmc.edu)
Sequence analysis tools accessed from the Genome Context View menu use the current genomic region as input. (plantgdb.org)
We performed full-length viral sequence analysis in 18 patients with chronic HCV subtype 3a infection and assessed genomic viral variability in comparison to other HCV subtypes. (lonelyjoeparker.com)
Following crRNA and tracrRNA hybridization, SpCas9 is targeted to genomic loci matching a 20-nt guide sequence within the crRNA, immediately upstream of a required 5′-NGG protospacer adjacent motif (PAM) 11 . (cdc.gov)
Site-directed mutagenesis of the proximal promoter region showed that two GC-rich sequence elements are essential for transcriptional activity in myeloid cells. (uni-frankfurt.de)

Here, we show that alterations in RNA splicing patterns across the human transcriptome that occur in conditions of restricted cellular PRPF8 abundance are defined by the altered splicing of introns with weak 5′ splice sites. (biomedcentral.com)
Thus, results from the combination in WAPPC3 of intact 5' and 3' WAP UTR with the cDNA of hPC suggests that introns are not necessary to enable high level expression in the mammary gland when using WAP regulatory elements. (vt.edu)

The ability of the upstream regions to bind nuclear factors was also evaluated using gel-shift analysis. (aspetjournals.org)

We first identified the transcription start site of cNANOG by 5′-rapid amplification of cDNA ends PCR analysis. (biomedcentral.com)
In contrast to past studies with WAP-cDNA fusion transgenes where the maximal expression was about 5% of endogenous WAP expression, the WAPPC3 transgene gave maximal expression which was about 30% of endogenous WAP expression. (vt.edu)

The proximal region of the cNANOG promoter contains a positive transcriptional regulatory element (CCAAT/enhancer-binding protein ( CEBP )-binding site) in ESCs. (biomedcentral.com)
Therefore, identification of regulatory elements within the promoter region is considered crucial to understand the mechanism underlying transcriptional regulation in specific cell types. (biomedcentral.com)
DNA accessibility for the transcriptional machinery is regulated in part by chemical modifications to histones that can alter chromatin structure or nucleosome positioning, and by direct DNA modifications that can alter transcription factor-binding sites [ 5 ]. (biomedcentral.com)

The Streptococcus pyogenes Cas9 (SpCas9) nuclease can be efficiently targeted to genomic loci by means of singleguide RNAs (sgRNAs) to enable genome editing 1 - 10 . (cdc.gov)
100 predicted genomic off-target loci in 293T and 293FT cells. (cdc.gov)

Genomic sequencing verified small deletions at the targeted locus. (biomedcentral.com)
Using CIS-ANALYST, the distribution of Bcd, Cad, Hb, Kr, and Kni binding sites were examined in a 1-Mb genomic region surrounding the well-characterized eve locus at a site_p value of 0.0003. (sdbonline.org)

Top row shows poliovirus genetic organization, with the main open reading frame flanked by the 5′ and 3′ untranslated regions (UTRs). (cdc.gov)
Recent high-impact research has shown the genomic/genetic differences between cancer and normal cells using methods such as next-generation sequencing [ 1 , 2 ]. (intechopen.com)
The vector pSelAct-KO is a recombination based, markerless knockout system that uses dual selection to engineer seamless deletions of a region of interest, providing opportunities for repeated higher-order genetic knockouts. (biorxiv.org)

C) Similarity plot drawn by comparing the sole genome of pattern 5 with genomes of patterns 3 (green), 4 (red), and 6 (blue) in the 3′ half of the genome. (cdc.gov)
Direct evidence for the presence of these viruses in human genital tumours is the finding that a small proportion (about 10%) retain fragments of virus DNA from different regions of the virus genomes. (microbiologyresearch.org)

Molecular Phylogenetics and Evolution , 5 (1), 2-12. (urosario.edu.co)

Depending on the desired mutation, several experimental options exist in the isolation of clonal lines, such as selection with introduced markers, or screening by PCR amplification of genomic DNA. (biomedcentral.com)

Primer extension experiments demonstrated the existence of two possible transcription initiation sites at nucleotide -29 and 32 position, 5' to the start of the translation. (elsevierpure.com)
5 , 6 In concordance with the role of nodal cilia in L-R asymmetry, mutations in the motor proteins Kif3A and Kif3B, and the transcription factor Foxj1 in the mouse have demonstrated that ciliary motility is important for L-R asymmetry. (bmj.com)
By using published DNA binding specificity data for five transcription factors active in the early Drosophila embryo, genomic regions containing unusually high concentrations of predicted binding sites were identified for these factors. (sdbonline.org)
As these adaptive genomic regions are largely devoid of DNA methylation and of Hp1- and Dim5-associated heterochromatin, the differential transcription is likely caused by pleiotropic effects rather than by differential DNA methylation. (biomedcentral.com)
We show that this region contains a Notch-responsive cis-regulatory module that directs numb transcription in the pIIa and pIIIb cells of the bristle lineage. (silverchair.com)
Analysis of transcription factor (TF) and ChIP- seq datasets identified overlap of 70 SNPs with TF binding regions of relevant lung cell lines (e.g. (cdc.gov)

DNA methylation is an important epigenetic control mechanism that in many fungi is restricted to genomic regions containing transposable elements (TEs). (biomedcentral.com)
Cytosine methylation can occur in symmetric CG or CHG genomic contexts, or in the asymmetric CHH genomic context, where H stands for either A, C or T. In general, 5mC occurs more commonly at symmetric sites because maintenance methylation can cause methylation of daughter strands during DNA-replication, whereas asymmetric sites require de novo methylation [ 7 ]. (biomedcentral.com)
In mammals, DNA methylation is largely restricted to CG sites, while plants and fungi show methylation in each of the genomic contexts [ 8 ]. (biomedcentral.com)
Dim2 operates in a complex with Heterochromatin Protein-1 (Hp1) that recognizes and directs DNA methylation to genomic regions marked by tri-methylation of histone 3 lysine 9 (H3K9me3) that is deposited by the histone methyltransferase Deficient In Methylation-5 (Dim5) [ 11 , 12 ]. (biomedcentral.com)

Allele-specific polymerase chain reaction analysis of genomic DNA from 90 Chinese individuals revealed that the CYP2D6Ch1 allele was the most common one and its distribution correlated well with a higher metabolic ratio for debrisoquine. (aspetjournals.org)
Q5U Hot Start High-Fidelity DNA Polymerase is a modified version of Q5 ® High-Fidelity DNA Polymerase, a novel thermostable DNA polymerase that possesses 3′ to 5′ exonuclease activity, and is fused to a processivity-enhancing Sso7d domain. (neb.com)
Amplification of bisulfite-converted human genomic DNA targets using Q5U Hot Start High-Fidelity DNA Polymerase (Q5U), Phusion U Hot Start DNA Polymerase (P) and KAPA Hifi HotStart Uracil+ ReadyMix PCR Kit (K). Amplicon name and sizes are indicated above the gel. (neb.com)

The resulting plasmid and the wild-type BmNPV genomic DNA were cotransfected into BM-N cells, and a recombinant virus was isolated by the limiting dilution method. (microbiologyresearch.org)
We developed permissR, an R package to identify permissive sites for chromosomal integration, which can be used in conjunction with pSelAct-Express, a non-replicating integrative plasmid that enables recombination into a permissive genomic location. (biorxiv.org)

The importance of S. commune as a model system is also exemplified by the fact that its recombinant DNA constructs will express in other mushroom-forming fungi 5 . (nature.com)

To study the genomic divergences among hominoids and to estimate the effective population size of the common ancestor of human and chimpanzee we selected 53 autosomal intergenic noncoding DNA segments from the human genome and sequenced them in a human, chimpanzee, gorilla, and orangutan. (ncl.edu.tw)

Spliced alignment of user-specified transcript datasets to genomic DNA from any region in CsGDB. (plantgdb.org)

Some modeling analyses suggest 5 separate events are required in colon cancer. (medscape.com)

For any specified genomic region , download genomic DNA (FASTA format), all aligned/computed transcripts or proteins (FASTA format), or all genome annotations (GenBank, GFF3 or EMBL format). (plantgdb.org)

This catalyzes endonucleolytic cleavage of DNA yielding 5'-phosphodi- and oligonucleotide end-products. (lookformedical.com)
Due to its particularly simple makeup, the type II CRISPR/Cas system of Streptococcus pyogenes has been adapted for genomic editing with great success: a single protein, Cas9, is required for crRNA binding and cleavage, and the RNA components have been engineered into a single guide RNA (sgRNA) [ 23 ]. (biomedcentral.com)

We also found an A + T rich region between nucleotide -505 and -390 which contained twenty-two AAAAT tandem repeats. (elsevierpure.com)

These motifs arise because of particular requirements on the structure of specific region(s) of a protein which may be important, for example, for their binding properties or for their enzymatic activity. (open-bio.org)

It was shown that the H19 ICR displays unique chromatin conformation features with nuclease hypersensitive sites in linker elements flanked by positioned nucleosomes on the maternally derived allele. (kb.se)

Transgene expression reaches peak levels during development, and persists at high levels in particular adult brain regions, such as the hippocampus and olfactory bulb. (harvard.edu)
Direct binding of ZFP143 to the proximal region of the NANOG promoter regulates NANOG expression by modulating OCT4 binding [ 24 ]. (biomedcentral.com)
Expression of eGFP by pSelAct-Express was verified in two candidate permissive regions predicted by permissR in C. michiganensis . (biorxiv.org)

They consisted of flanking conserved hydrophobic amino acids and central variable residues. (lonelyjoeparker.com)
A 5-amino-acid insertion found only in genotype 3a and a putative glycosylation site is contained within HVR575. (lonelyjoeparker.com)

BmNPV genomic DNA codes polyhedrin which is a major protein of inclusion bodies and is mass- produced in infected silkworm larvae. (microbiologyresearch.org)
Two compounds, Compound 1 (1,4-dihydrophenanthrolin-4-one-3-carboxylic acid) and Compound 5 [8-(N-butyl-N-ethylcarbamoyl)-1,4-dihydrophenathrolin-4-one-3-carboxylic acid], with comparable potencies in vivo, were chosen to investigate the effect of the inhibition of the hydroxylation of newly synthesized uterine collagen on the turnover of this protein in vivo. (embl.de)
Two novel regions of intragenotypic hypervariability within the envelope protein E2, of HCV genotype 3a, were identified. (lonelyjoeparker.com)
In particular, the intricate nature of red vs. black color patterns such as facial markings on a Doberman Pinscher or the saddle on a German Shepherd Dog are not easily explained by what was known about the mouse melanocortin system, in which the paracrine signaling molecule Agouti signaling protein (ASIP) causes overlying hair follicle melanocytes to switch from making eumelanin to pheomelanin (5). (springernature.com)

Or, to access the same tools without a genomic context, use CsGDB left menubar Tools links. (plantgdb.org)

G variation, located in the 3′-untranslated region, could be associated with low transcript abundance. (aspetjournals.org)

The WAPPC1 and WAPPC2 transgenes expressed up to about 10 μg/ml recombinant hPC in mouse milk while WAPPC3 expressed 30-300 (n=10, n=5, n=11, number of founder lines evaluated for each transgene, respectively). (vt.edu)

Further defining the functional significance of these regions may have important implications for genotype 3a E2 virus-receptor interactions and for vaccine studies that aim to induce cross-reactive anti-E2 antibodies. (lonelyjoeparker.com)

B) Schematic representation of the genomic patterns of the VDPVs. (cdc.gov)

Then, we measured the promoter activity of various 5′ flanking regions of cNANOG in chicken PGCs and ESCs using the luciferase reporter assay. (biomedcentral.com)

In addition, TFs generally initiate and guide cell fate such as lineage progression and control the stability of cell differentiation [ 5 ]. (biomedcentral.com)
NGS was performed in 91 workers with DA (cases) and in 293 subjects from the 1,000 genomic (1KG) control data set. (cdc.gov)

isolate ="MUMH29s" / mol_type ="genomic DNA" / organism ="Microsphaera trifolii var. (nig.ac.jp)

One critical step involves recruitment of the pre-assembled U4/U6.U5 tri-snRNP to Complex A, which engages 5′ and 3′ splice sites, to form the pre-catalytic Complex B. Complex B then undergoes profound structural and conformational changes that lead to catalytic activation and conversion to Complex B act , which initiates catalysis and nucleates the formation of Complex C, which completes the splicing reaction [ 3 , 4 ]. (biomedcentral.com)
When the 1-Mb region surrounding eve was searched for dense clusters of predicted high-affinity sites (at least 13 Bcd, Cad, Hb, Kr, or Kni sites in a 700-bp window), three discrete regions were identified. (sdbonline.org)
The same clustering criteria that were successful for identifying CRMs in eve (700-bp regions with at least 13 predicted binding sites) identified clusters overlapping 14 of these 19 known CRMs (Berman, 2002). (sdbonline.org)

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