Sentences with phrase «from exons»

The Punc - 7S promoter sequences in intron 3 were eliminated by substituting this region with unc - 7 cDNA sequence from exons 2 — 6 (unc -7-2cDNA6; Figure 3E).

Primers were chosen from exons separated by large introns, when possible, and PCR reaction quality and specificity were verified by gel electrophoresis and melting - curve dissociation analysis of the amplified product.

The study, led by a team in The Research Institute at Nationwide Children's Hospital, is the first of its kind to show these results from an exon - skipping drug — a class of therapeutics that allows cells to skip over missing parts of the gene and produce protein naturally.

Intron coordinates were generated from Exon coordinates using a custom Perl script and BEDTools [20] v2.14.3.

Not exact matches

The most compelling evidence for this conclusion came from the finding that the protein - encoding information of c - src is divided into several separate domains, called exons, by intervening regions known as introns.

This finding suggests that the homologous region may have resulted from a duplication of an ancestral gene and that the two genes evolved further by recruitment of exons from other genes, which provided the specific functional domains of the LDL receptor and the EGF precursor.

As a consequence of differential RNA splicing, mRNAs containing different combinations of exons can be produced from the same gene.

(B) Species tree inferred from high — base composition variance exons (n = 830 genes), graphed similarly as in (A).

Trees created from analysis of the first and second codon positions (exon c12) of the TENT data also had lower levels of BS (~ 39 to 64 %) but with more topological differences on the deep branches (Figs. 2, 4C, and 5A), yet all but one of the fully resolved relationships (local difference in egret + ibis + pelican) were congruent with the TENT (Fig. 5B).

We further investigated the source of the conflict in the protein - coding genes (SM11) and found that trees using all codon positions from the 10 % most compositionally homogeneous (low - variance) exons (n = 830) were most congruent with the c12 tree and, thus, more similar to the TENT than to the c123 tree (Figs. 2 and 6A; cladograms in fig.

Another related paper published from the Wang lab indicated that DAZAP1 could bind to the introns as well as exons, but the molecular mechanism of DAZAP1 function was less understood at that time.

Conversely, trees using all codon positions from the 10 % most compositionally heterogeneous (high - variance) genes (n = 830) were more congruent with the exon c123 and c3 trees (Figs. 2 and 6B and fig.

To estimate the avian timetree with genomic - scale data, we used first and second codon positions from 1156 clock - like exon genes (which do not strongly exhibit the above protein - coding compositional bias), calibrated with 19 conservatively chosen avian fossils (plus nonavian outgroups) as minimum bounds for lineage ages (with a maximum - bound age constraint of 99.6 Ma for Neornithes), in a Bayesian autocorrelated relaxed clock method using MCMCTREE (77) on the fixed ExaML TENT topology (SM12).

No single intron, exon, or UCE locus from our TENT data set had an estimated topology identical to the ExaML TENT or MP - EST * TENT (fig.

From these efforts, we identified a high - quality orthologous gene set across avian species, consisting of exons from 8251 syntenic protein - coding genes (~ 40 % of the proteome), introns from 2516 of these genes, and a nonoverlapping set of 3769 ultraconserved elements (UCEs) with ~ 1000 bp of flanking sequenFrom these efforts, we identified a high - quality orthologous gene set across avian species, consisting of exons from 8251 syntenic protein - coding genes (~ 40 % of the proteome), introns from 2516 of these genes, and a nonoverlapping set of 3769 ultraconserved elements (UCEs) with ~ 1000 bp of flanking sequenfrom 8251 syntenic protein - coding genes (~ 40 % of the proteome), introns from 2516 of these genes, and a nonoverlapping set of 3769 ultraconserved elements (UCEs) with ~ 1000 bp of flanking sequenfrom 2516 of these genes, and a nonoverlapping set of 3769 ultraconserved elements (UCEs) with ~ 1000 bp of flanking sequences.

«Most often when material from introns is improperly included with exons, the result is nonsense proteins that go on to quickly degrade, meaning that cancer may use this strategy to downregulate the production of certain anti-cancer proteins,» Tan says.

Specifically, splicing removes pieces of intron and exon regions from the RNA.

The exact mutation varies from patient to patient but in 65 percent of cases, the dystrophin gene is missing large sections of DNA called exons, which carry the instructions for protein production.

If the RNA has different exons spliced in and out of it, then different proteins can be made from this RNA.

The research, which appears online Aug. 1 in the journal Annals of Neurology, is the first study from a double - blind controlled randomized trial of an exon - skipping agent to provide conclusive proof based on the standard six - minute walk test used to measure muscle function in patients with Duchenne muscular dystrophy (DMD), the most common form of muscular dystrophy in children.

Although «cDNA retains the naturally occurring exons of DNA... it is distinct from the DNA from which it was derived,» the court wrote.

Primary miRNA transcripts, or pri - miRNAs, are quickly processed into mature miRNAs from hairpin structures located in the exons or introns of pri - miRNA transcripts.

(Mixture - of - Isoforms) for isoform quantitation using RNA - Seq is a probabilistic framework that quantitates the expression level of alternatively spliced genes from RNA - Seq data, and identifies differentially regulated isoforms or exons across samples.

The team led by biomedical engineering professor Charles A. Gersbach used a mouse model suffering from a mutated exon of the dystrophin gene, programming CRISPR / CAS9 — a bacterial - protein derived process of cutting and pasting DNA portions — to snip out the defective exon.

Analyses were restricted to CDSs from Ensembl v72, as well as 10 bp upstream and downstream of each exon.

A transcribed genomic sequence that gives rise to one or more proteins with shared exons was scored as one transcription unit, and its length was taken from the position of RNA initiation to that of the site of polyadenylation, as measured on the underlying genomic sequence.

We considered genes with at least 5 reads mapping in exons and from all biotypes in the annotation.

From this subset of selected exons we have then performed correlation analysis of the PSI value with the PMI value for each tissue.

The C to A nucleotide change in exon 3 of A / J (SNP rs29358506) mice causes a nonconservative amino acid change, from histidine (H) to asparagine (N) at position 55 of the protein (H55N).

Using this technology, we screened 31 patient samples across an array containing a total of 162 exons for five disease genes and detected copy - number changes, ranging from whole - gene deletions and duplications to single - exon deletions and duplications, in 100 % of the cases.

In contrast to gene expression, there is a substantial sharing of exons among the top affected tissues (those with ≥ 20 significant exons), with the tissue pairwise overlap ranging from 43 % to 82 %, representing 22 to 76 shared exons.

The gbp1, gbp2 ex67 mutant lacks 1525 bp from the P - element insertion site, which includes the entire gbp1 gene and one - third of the second exon of gbp2 gene.

Sequences for 54 nuclear genes were taken from Perelman et al.'s [12] nexus file with modifications to eliminate problems with probable contaminants and misidentified sequences (Table S2); sequences for 15 additional nuclear genes (ABO, CXCR4, CXCR5, Epsilon globin, FGA, IRBP intron 1, IRBP intron 3, MC1R, NRAMP, PRNP, VWF intron 11) were obtained from GenBank; and new sequences (JX856181 - JX856283, JX869897 - JX869930) for exons of four nuclear genes (GHR, IRBP, VWF, TTN) were combined with previously published GenBank sequences for these loci.

In CCHa2 - RKO51 - 2, a 4 - kb deletion spanning exons 2 through 6 removes a region from the initiating methionine through the middle of 7th transmembrane domain.

We designed primers with built - in SalI sites to amplify a 2 - kb left arm next to exon 3, and primers with built - in XhoI and NotI sites to amplify a 5.9 - kb right arm from 129svj mouse genomic DNA.

The vast majority of receptor genes contain several exons and it is common to observe differential inclusion of these, diversifying the transcript set produced from each gene.

Primers flanking exons 14, 15 and the activation loop region of exon 20 of the FLT3 gene, and exon 12 of the NPM1 gene are used to amplify DNA extracted from a patient sample.

RT - PCR analysis of RNA from mouse embryonic and adult gonads using primers corresponding to either exons 3 and 9 (upper panel, 501 - bp band) or exons 3 and 12 (lower panel, 847 - bp and 712 - bp bands) reveals that full - length Bol1 is only expressed in postnatal testes, while Bol2 lacking exon 11 is also detectable at low levels throughout gonadal development in addition to its high adult testis expression.

Coding exons, exon — intron junctions, and 5 ′ - and 3 ′ - UTRs of the psq gene were sequenced in genomic DNA from psqrum homozygous flies and from flies carrying the parental chromosome (FRTG13 c px sp; Luschnig et al. 2004).

We amplified cDNA from wild - type and mutant ovaries (and genomic DNA as a control) using primers located in the exons flanking the mutation.

Hex cDNA tagged with a recognition site for the bacterial BirA ligase (B), followed by an artificial IRES sequence composed of a tandem array of reiterated 9 bp elements from the Gtx promoter and DNA encoding the fluorescent reporter, Venus, was inserted into the first exon of the Hex locus.

Using our own data and publically available data from array comparative genomic hybridization (aCGH), we identified a minimal deletion for the cardiomyopathy associated with del1p36 that included only the terminal 14 exons of the transcription factor PRDM16 (PR domain containing 16), a gene that had previously been shown to direct brown fat determination and differentiation.

Correction of dystrophin expression in cells from Duchenne muscular dystrophy patients through genomic excision of exon 51 by zinc finger nucleases.

Splicing the process by which introns are removed from the pre-mRNA molecules and remaining exons are joined together, forming the final messenger RNA (mRNA) that is translated into proteins.

BED files with the genomic coordinates for CpG islands, CpG island shores, exons, segmental duplications, self chains (downloaded on 09/21/2011), promoters, repeats and mammal conservation (downloaded on 12/19/2011) were downloaded from the UCSC Genome Bioinformatics Site (http://genome.ucsc.edu/).

Clinical trials have used oligonucleotide exon skipping (OEN) to remove mutated exons from the dystrophin transcript.

Mouse embryonic stem cells with one allele of Melk inserted with lacZ and neomycin - resistance genes between exon 2 and 3 were obtained from the Knockout Mouse Project (KOMP; ID: CSD33136).

Sequence analysis of the 283 bp crd3 - affected amplicon from primer pair 7 showed that exons 15 and 16 are absent from affected cDNA.

To further characterize canine ADAM9, 33 primer pairs were designed to amplify and sequence the genomic interval between exon 14 and exon 17 from one normal and two affected dogs (Table 4).

PCR amplicons from COLQ exon 14 are 470 bp in size and cleaved into 204 and 266 bp fragments in the presence of c. 1010T > C. Three clinically normal littermates were identified as carriers, denoted by semi-filled icons.