Exons. Medical search. Frequent questions (1)

An exon is any part of a gene that will form a part of the final mature RNA produced by that gene after introns have been removed by RNA splicing. (wikipedia.org)
The term exon refers to both the DNA sequence within a gene and to the corresponding sequence in RNA transcripts. (wikipedia.org)
Across all eukaryotic genes in GenBank, there were (in 2002), on average, 5.48 exons per protein coding gene. (wikipedia.org)
Mature mRNAs originating from the same gene need not include the same exons, since different introns in the pre-mRNA can be removed by the process of alternative splicing. (wikipedia.org)
Exon trapping or 'gene trapping' is a molecular biology technique that exploits the existence of the intron-exon splicing to find new genes. (wikipedia.org)
The first exon of a 'trapped' gene splices into the exon that is contained in the insertional DNA. (wikipedia.org)
This new exon contains the ORF for a reporter gene that can now be expressed using the enhancers that control the target gene. (wikipedia.org)
DBASS3/5 Exitron Exon-intron database Exon shuffling Interrupted gene Outron Twintron Untranslated region (UTR) Gilbert W (February 1978). (wikipedia.org)
The restriction analysis and partial sequencing of the gene shows that it contains (1) four alternatively spliced exons previously described in rodent and bovine but not in human tau cDNAs and (2) two CpG islands, one associated with the promoter region, the other with exon 9. (nih.gov)
SimpleChIP ® Human DNAJB9 Exon 1 Primers contain a mix of forward and reverse PCR primers that are specific to exon 1 of the human DnaJ homolog subfamily B member 9 gene. (cellsignal.com)
Patients with MET exon 14 skipping mutations or MET amplifications, according to the gene copy number in tumor tissue, were enrolled. (onclive.com)
Our results show that one out of 60 bulls tested exhibited polymorphism (G→T) at position 559 in exon 4 of SLC35A3 gene. (researchgate.net)
To the our best of knowledge, this is the first study to report the existence of homozygous and heterozygous mutations at positions 554, 555 and 559 in exon 4 of SLC35A3 gene in Indian Holstein cattle. (researchgate.net)
exon 4 of SLC35A3 gene. (researchgate.net)
554, 555 and 559 in exon 4 of SLC35A3 gene in Indian Holstein cattle. (researchgate.net)
The gene encoding the insect nicotinic acetylcholine receptor (nAChR) α6 subunit, target of the bio-insecticide spinosad, is one example of this and expands protein diversity via alternative splicing of mutually exclusive exons. (datadryad.org)
Our results demonstrate that the intrinsic capacity of the α6 gene to generate transcript diversity via alternative splicing can be readily exploited during the evolution of resistance and identifies exon skipping as a molecular alteration conferring insecticide resistance. (datadryad.org)
We identified a novel exonic mutation which causes exon skipping in the mitochondrial acetoacetyl-CoA thiolase (T2) gene from a girl with T2 deficiency (GK07). (jci.org)
At the gene level, a C to T transition causing Gln272 to termination codon (Q272STOP) was identified within exon 8, 13 bp from the 5' splice site of intron 8 in the paternal allele. (jci.org)
When we compare the gene between vertebrate species and look for conserved sequence we find that there are strong signals of sequence conservation that line up with the exons. (evcforum.net)
Here we report a silent variant found in exon 2 in the F8 gene in a 47-year-old patient with a previous von Willebrand disease (VWD) type 1 diagnosis. (lu.se)
I am not familiar with the Gtex portal, but looks like they really count all the exons of a gene no matter from which transcript they come. (biostars.org)
I want to download the sequences of all the exons for each human gene. (biostars.org)
my bed file is not in bed12 and each exon is in a separate row (though the name column of the bed file is the gene ID). (biostars.org)
Comparison of our mouse exon-skipping events to previously detected human exon-skipping events on chromosome 22 by Hide et al.2001, has revealed that mouse and human exon-skipping events were never observed together within an orthologous gene-pair. (uwc.ac.za)
Although the transcript identity between mouse and human orthologous transcripts were high (greater than 80% sequence identity), the exon order in these gene-pairs may be different between mouse and human orthologous genes. (uwc.ac.za)
Our conclusion that the mouse exon-skipping frequency may be lower than the human estimate remains to be tested with a larger mouse multi-exon gene set. (uwc.ac.za)
How can we get the exon co-ordinates of the variants from MAF file (Mutation Annotation Format), if we have chromosome location of the genes and gene symbol. (bioconductor.org)
Emerging therapeutic approaches include gene transfer therapy using adeno-associated virus (AAV) vectors, and exon skipping agents. (nova.edu)
However, researchers have found that DNA variations outside the exons can affect gene activity and protein production and lead to genetic disorders--variations that whole exome sequencing would miss. (medlineplus.gov)
These primers amplify approximately 495 bp of exons and introns at the 5' end of the β-tubulin gene. (cdc.gov)
A 133 bp fragment, spanning exon 11 of the APC gene was amplified, and Rsal digestion of the PCR product defined the alleles as either homozygous 133 bp (Rsa(-/-)) or 87 and 46 bp (Rsa(+/+)) fragments, and heterozygous (Rsa(+/-)) exhibiting the three fragments. (who.int)

Exonization is the creation of a new exon, as a result of mutations in introns. (wikipedia.org)
Among patients with non-small cell lung cancer and MET exon 14 skipping mutations, an overall response rate of approximately 41% has been seen. (onclive.com)
What we learned is that this drug elicits meaningful responses in patients who harbor MET exon 14 skipping mutations. (onclive.com)
I would consider identifying MET exon 14 skipping mutations up front and using this drug in the first line. (onclive.com)
The key takeaways for me are this is an exciting advance for the field and is another drug that can and should be used for patients with MET exon 14 skipping mutations. (onclive.com)
On September 15, 2021, the Food and Drug Administration granted accelerated approval to mobocertinib (Exkivity, Takeda Pharmaceuticals, Inc.) for adult patients with locally advanced or metastatic non-small cell lung cancer (NSCLC) with epidermal growth factor receptor (EGFR) exon 20 insertion mutations, as detected by an FDA-approved test, whose disease has progressed on or after platinum-based chemotherapy. (fda.gov)
Approval was based on Study 101, an international, non-randomized, open-label, multicohort clinical trial (NCT02716116) which included patients with locally advanced or metastatic NSCLC with EGFR exon 20 insertion mutations. (fda.gov)
NSCLC patients with MET exon 14 skipping mutations are typically 70 years of age or older. (esmo.org)
In their article, published in the NEJM, they reported the results in patients with MET exon 14 skipping mutations. (esmo.org)
The authors concluded that their results show that the selective MET inhibitor tepotinib has durable clinical activity in patients with NSCLC with MET mutations associated with exon 14 skipping. (esmo.org)
Imatinib in systemic mastocytosis: a phase IV clinical trial in patients lacking exon 17 KIT mutations and review of the literature. (qxmd.com)
Resistance to imatinib has been recurrently reported in systemic mastocytosis (SM) carrying exon 17 KIT mutations. (qxmd.com)
We evaluated the efficacy and safety of imatinib therapy in 10 adult SM patients lacking exon 17 KIT mutations, 9 of which fulfilled criteria for well-differentiated SM (WDSM). (qxmd.com)
Absence of exon 17 KIT mutations was confirmed in highly-purified BM MCs by peptide nucleic acid-mediated PCR, while mutations involving other exons were investigated by direct sequencing of purified BM MC DNA. (qxmd.com)
Because most known mutations that cause disease occur in exons, whole exome sequencing is thought to be an efficient method to identify possible disease-causing mutations. (medlineplus.gov)

Just as the entire set of genes for a species constitutes the genome, the entire set of exons constitutes the exome. (wikipedia.org)
In humans, like protein coding mRNA, most non-coding RNA also contain multiple exons In protein-coding genes, the exons include both the protein-coding sequence and the 5′- and 3′-untranslated regions (UTR). (wikipedia.org)
Often the first exon includes both the 5′-UTR and the first part of the coding sequence, but exons containing only regions of 5′-UTR or (more rarely) 3′-UTR occur in some genes, i.e. the UTRs may contain introns. (wikipedia.org)
However, these sorts of definitions only cover protein-coding genes, and omit those exons that become part of a non-coding RNA or the untranslated region of an mRNA. (wikipedia.org)
Examination of human tau mRNA indicates that the human cerebrocortical splicing pattern differs from that previously reported for the murine and bovine tau mRNAs, despite conserved exon organization in all three genes. (nih.gov)
Genes themselves consist of protein-coding exons and non-coding introns. (jove.com)
Because longer genes encode longer BPRPs, we investigated the possibility of exon sequencing BPRP alleles encoded by PRB1 and PRB2. (umich.edu)
Many genes increase coding capacity by alternate exon usage. (datadryad.org)
Just for clarity, exons are segments of eukaryotic genes that are stitched together to make a mature mRNA molecule that is then translated into protein. (evcforum.net)
Fu, P & Evans, B 1992, ' A novel PCR method for amplifying exons (or genes) over intragenic (or intergenic) regions in the genome ', Nucleic Acids Research , vol. 20, no. 11. (monash.edu)
Several alternative splicing surveys have confirmed the frequent occurrence of exon skipping in human genes. (uwc.ac.za)
However, the occurrence of exon skipping in mouse genes has not yet been extensively examined. (uwc.ac.za)
Recent improvements in mouse genome sequencing have permitted the current study to explore the occurrence of exon skipping in mouse genes orthologous to human genes on chromosome 22. (uwc.ac.za)
A low number (5/72 multi-exon genes) of mouse exon-skipped genes were captured through alignments of mouse ESTs to mouse genomic contigs. (uwc.ac.za)
Exon-skipping events in two mouse exon-skipped genes (GNB1L, SMARCB1) appear to affect biological processes such as electron and protein transport. (uwc.ac.za)
These factors resulted in a large number (112/269) of mouse transcripts lacking matches to mouse genomic contigs and nearly half (12/25) of the mouse multi-exon genes, which have matching Ensembl transcript identifiers, have under-predicted exons. (uwc.ac.za)
However, when compared to a higher estimate (52/347) of exon skipping in human genes for chromosome 22 produced under similar conditions by Hide et al.2001, it is possible that our mouse exon-skipping frequency may be lower than the human frequency. (uwc.ac.za)
However, the mouse exon-skipping frequency may represent the highest estimate that can be obtained given that the current number (87) of mouse genes orthologous to chromosome 22 in Ensembl (v1 30th Jan. 2002) does not deviate significantly from our total number (72) of mouse multi-exon genes. (uwc.ac.za)
Certain combinations of common variants in exon 3 of OPN1LW and OPN1MW, the genes encoding the apo- protein of the long- and middle-wavelength sensitive cone photoreceptor visual pigments in humans , induce splicing defects and have been associated with dyschromatopsia and cone dysfunction syndromes . (bvsalud.org)
In BASE, reporters also refer to Affymetrix Probeset ID but reporters can be used to describe genes, transcripts, exons or any other sequence entity of biological relevance. (lu.se)
Reporters are used to represent genes, transcripts, exons and therefore come in their thousands. (lu.se)

Splicing can be experimentally modified so that targeted exons are excluded from mature mRNA transcripts by blocking the access of splice-directing small nuclear ribonucleoprotein particles (snRNPs) to pre-mRNA using Morpholino antisense oligos. (wikipedia.org)
Introns are excised once the sequence is transcribed to mRNA, leaving only exons to code for proteins. (jove.com)
Sequencing of the α6 subunit cDNA from spinosad selected and unselected strains of T. absoluta revealed all Taα6 transcripts of the selected strain were devoid of exon 3, with comparison of genomic DNA and mRNA revealing this is a result of exon skipping. (datadryad.org)
This substitution was thought to alter the secondary structure of T2 pre-mRNA around exon 8 and thus impede normal splicing. (jci.org)
Here we report a class of mRNA granules in human neuronal processes that are enriched in the nuclear cap-binding protein complex (CBC) and exon junction complex (EJC) core components, Y14 and eIF4AIII. (frontiersin.org)
In addition to the cis -elements in its 3′UTR and trans -acting factor Staufen, posterior localization of oskar mRNA requires deposition of exon junction complex (EJC) in its first exon through splicing ( Hachet and Ephrussi, 2004 ). (frontiersin.org)
Here, we find that many aberrant exonic SS are efficiently silenced by the exon junction complex (EJC), a multi-protein complex that is deposited on spliced mRNA near the exon-exon junction. (uni-koeln.de)
Current DMD therapeutics use phosphorordiamidate morpholino oligomers (PMO) to skip over the frame-shifting exon during the splicing of the dystrophin pre-mRNA, resulting in translation of a truncated dystrophin protein product. (gene-tools.com)

In patients with advanced non-small cell lung cancer (NSCLC) with a confirmed MET exon 14 skipping mutation, the use of tepotinib was associated with a partial response in approximately half the patients. (esmo.org)
A study presented today at the IASLC World Conference on Lung Cancer 2022 in Vienna disclosed the clinical-relevant intertumoural heterogeneity of non-small cell lung cancer (NSCLC) driven by MET exon 14 skipping. (ecancer.org)
MET exon 14 skipping, as a rare driver for non-small cell lung cancer (NSCLC), can be successfully targeted by MET specific tyrosine kinase inhibitors (TKI) like savolitinib, tepotinib, and capmatinib. (ecancer.org)
Recent clinical trials of MET selective TKIs displayed encouraging clinical efficacy but nearly half of NSCLC patients with MET exon 14 skipping did not benefit from MET-TKI treatment, which indicated biological heterogeneity in NSCLCs driven by METex14 skipping. (ecancer.org)
En este video, el Dr. Rodríguez nos actualiza sobre objetivos moleculares emergentes en NSCLC: fusiones RET, MET, KRAS, inserciones del exón 20 de EFGR. (cancergrace.org)

She was also involved in mouse studies to develop antisense-mediated exon skipping therapies for DMD. (exonskipping.nl)

To test the hypothesis that miR-146a is inhibitory to exon skipping dystrophin restoration, we generated a novel DMD double knockout mouse model with body-wide miR-146a deletion ( 146aX mice) and administered an exon 51 skipping PMO into the tibialis anterior (TA) muscles of mdx52 and 146aX mice. (gene-tools.com)
These data demonstrate genetic deletion of miR-146a is sufficient to increase dystrophin rescue via exon skipping. (gene-tools.com)

Importantly, between these beginning and end points lie areas called introns and exons, both of which are reflected in the RNA product. (jove.com)
How does ID/creationism explain this pattern where introns and exons diverge as we move through these species? (evcforum.net)

Thus, in the study presented here, fifty-four individuals constituted a group comparable to DMD patients by exon 45 skip. (institut-myologie.org)

SFs contain ultraconserved poison exon (PE) sequences that exhibit greater identity across species than nearby coding exons, but their physiological role and molecular regulation is incompletely understood. (mendeley.com)
The role of exon sequences in the splicing mechanism is indicated by the exon skipping which occurred with an exonic mutation. (jci.org)
Then I tried to download directly Exon sequences, but the number of sequences was again larger the the number of exons should be and moreover several exon ids correspond to the same sequence. (biostars.org)
The issue you have with more sequences and exons is most likely due to alternative transcripts. (biostars.org)
Main factors contributing towards the low detection of mouse exon-skipping events include the lack of mouse transcripts matching to mouse genomic sequences and the under-prediction of mouse exons. (uwc.ac.za)
The capture of mouse exon-skipping events may increase as the quality and quantity of mouse genomic and transcript sequences improves. (uwc.ac.za)

Sanger sequencing of the patient's cDNA after nested polymerase chain reaction showed that the patient had both a normal transcript containing exons 1-4 and a defect transcript lacking exon 2. (lu.se)
I am not sure what you mean by "exon Numer" but I guess it is the rank (position of exon in a transcript, starting with 1 for the first one, even if not coding). (biostars.org)

Some non-coding RNA transcripts also have exons and introns. (wikipedia.org)
Because an exon can have different ranks in different transcripts. (biostars.org)
But the rank of this exon is 2 for both protein coding transcripts of SOD1. (biostars.org)
Applying minigene assays for all observed exon 3 haplotypes in the patients , we demonstrated that the novel exon 3 haplotype L-I-V-V-A induces a strong but incomplete splicing defect with 3-5% of residual correctly spliced transcripts. (bvsalud.org)

Given an Ensembl exon ID, how can I determine the exon number? (biostars.org)

Methods: All exons of PRB1 and PRB2 from 8 healthy adults were sequenced using an Illumina HiSeq 2000 (100 bp paired sequencing readouts with TruSeq™ Exome Enrichment Kit). (umich.edu)
Together, all the exons in a genome are known as the exome, and the method of sequencing them is known as whole exome sequencing. (medlineplus.gov)

While exon skipping therapies are promising, their potential has not been fully realized as increases in dystrophin protein have been minimal and highly variable in clinical trials. (gene-tools.com)
In dystrophin-deficient mice we find that co-injection of an exon skipping PMO with miR-146a but not a control sequence reduces the extent of dystrophin positive fibers. (gene-tools.com)
Our data suggests that antagomiR-mediated inhibition of miR-146a or other dystrophin targeting miRNAs could be a viable exon skipping DMD co-therapy and warrants further research. (gene-tools.com)
Even though exon skipping agents produce a smaller dystrophin protein, they effectively preserve a significant portion of its function. (nova.edu)

Since this RNA will be used to generate proteins, exons are denoted as coding regions, whereas introns are another example of non-coding material. (jove.com)
DNA and RNA sequencing analyses suggested that exon skipping did not result from genetic alterations in intronic or exonic cis-regulatory elements, but rather was associated with a single epigenetic modification downstream of exon 3a, and quantitative changes in the expression of trans-acting proteins that have known roles in the regulation of alternative splicing. (datadryad.org)

Exon skipping agents have clinical advantages over traditional therapies, such as corticosteroids, because they slow the progression of DMD in addition to relieving symptoms. (nova.edu)

CD44 is a transmembrane molecule appearing in numerous isoforms generated by insertions of alternatively spliced variant exons ( CD44v ) and having various binding partners. (nature.com)

Exon 3 Haplotype-Associated Splicing Defect in Patients with X-Linked Cone Dysfunction. (bvsalud.org)

Entrada Therapeutics has shared new data from a preclinical study evaluating ENTR-601-44 , an exon-skipping therapy set to target individuals with Duchenne amenable to exon 44 skipping. (parentprojectmd.org)
The company announced new non-human primate (NHP) data demonstrating durability of response through 12 weeks for ENTR-601-44, an EEV-conjugated phosphorodiamidate morpholino oligomer (PMO) for the potential treatment of people with Duchenne muscular dystrophy (DMD) who are exon 44 skipping amenable. (parentprojectmd.org)
Duchenne muscular dystrophy: Current treatment and emerging exon skipp" by Grant Patterson, Haley Conner et al. (nova.edu)

This study disclosed the clinical-relevant intertumoural heterogeneity of NSCLCs driven by MET exon 14 skipping. (ecancer.org)

For instance, in the human genome only 1.1% of the genome is spanned by exons, whereas 24% is in introns, with 75% of the genome being intergenic DNA. (wikipedia.org)
While the longest exon in the human genome is 11555 bp long, several exons have been found to be only 2 bp long. (wikipedia.org)
A single-nucleotide exon has been reported from the Arabidopsis genome. (wikipedia.org)
The low frequency of mouse exon skipping on chromosome 22 cannot be extrapolated to represent a genome-wide estimate due to the small number of observed mouse exon-skipping events. (uwc.ac.za)
These pieces, called exons, are thought to make up 1 percent of a person's genome. (medlineplus.gov)

Among them a promoter, exons, introns, and regulatory elements, which together help to determine protein expression in a cell. (jove.com)

The paternal allele was associated with exon 8 skipping at the cDNA level. (jci.org)

The term exon derives from the expressed region and was coined by American biochemist Walter Gilbert in 1978: "The notion of the cistron… must be replaced by that of a transcription unit containing regions which will be lost from the mature messenger - which I suggest we call introns (for intragenic regions) - alternating with regions which will be expressed - exons. (wikipedia.org)

The findings from the VISION study validate MET exon 14 skipping mutation as a therapeutic target and emphasize the importance of routine testing for these MET alterations by liquid or tissue biopsy. (esmo.org)

SimpleChIP ® Human DNAJB9 Exon 1 Primers were tested on DNA isolated from cross-linked cells using the SimpleChIP ® Plus Enzymatic Chromatin IP Kit (Magnetic Beads) #9005. (cellsignal.com)
PCR product melting curves were obtained for real-time PCR reactions performed using SimpleChIP ® Human DNAJB9 Exon 1 Primers. (cellsignal.com)
Exons 2 and 3 of the HLA-B locus were amplified with locus specific primers and the amplified DNA was arrayed onto seven replicate nylon membranes and immobilized by UV cross-linking. (cdc.gov)

It is then possible to compare groups of patients benefiting from a therapeutic jump from exon 45 or 51 with a corresponding BMD group, the idea being to have a predictive tool for the expected functional improvement. (institut-myologie.org)

can do what you want, if you supply a reference fasta and corresponding gtf or bed file of all exons ( http://bedtools.readthedocs.io/en/latest/content/tools/getfasta.html) . (biostars.org)

In vivo splicing experiments revealed that the exonic mutation caused partial skipping of exon 8. (jci.org)

The challenge for ID/creationists in this thread is to explain the divergence of exons and introns as measured by sequence comparisons between species. (evcforum.net)

See Exon Expression on the GTEx portal . (biostars.org)
All mouse, skipped exons were observed to have ubiquitous tissue expression. (uwc.ac.za)

Methods: We assessed DNA methylation at three CpG sites in the NOS2 exon 1 from blood from 201 welders. (cdc.gov)

Exon skipping cosegregated with spinosad resistance in survival bioassays, and functional characterization of this alteration using modified human nAChR α7, a model of insect α6, demonstrated that exon 3 is essential for receptor function and hence spinosad sensitivity. (datadryad.org)
As we can see, there is a lot of similarity between human and rhesus introns, but as we get to frogs and fish towards the bottom of the group the only similarities we find are in the exons. (evcforum.net)

Discussion on the FDA approval of capmatinib, a MET inhibitor, as treatment for patients with MET exon 14-mutated non-small cell lung cancer based on data demonstrated by the GEOMETRY mono-1 study. (onclive.com)
Capmatinib is a MET TKI [tyrosine kinase inhibitor] with very high affinity and excellent CNS [central nervous system] penetrance, so this is a huge step forward for our patients with MET exon 14 skipping non-small cell lung cancer. (onclive.com)
Le pourcentage de CD44 dans les lymphocytes T périphériques était significativement plus élevé chez les patients que chez les témoins, comme détecté par la cytométrie en flux. (who.int)
En outre, il y avait une aug- mentation significative de la forme soluble du c-kit dans le sérum des patients atteints de pemphigus vulgaire actif par rapport aux témoins. (who.int)

This form, MsrA(S), was generated using an alternative first exon. (unl.edu)
In addition, we found that mitochondrial and cytosolic forms of both MsrA and MsrB in Drosophila could be generated by alternative first exon splicing. (unl.edu)

The new data from a preclinical study evaluating ENTR-601-44 for the potential treatment of DMD, show robust exon 44 skipping in NHP biceps through 12 weeks following a single intravenous (IV) infusion, demonstrating durability of response (See Figure 1). (parentprojectmd.org)
These data build on a previously reported NHP study indicating robust exon 44 skipping across different muscle groups at 7 days following a single IV infusion. (parentprojectmd.org)

We have found that in a lot of cases we see peaks lining up with exons. (seqanswers.com)

The boxes represent the exons and the lines between the boxes are the introns. (evcforum.net)

The first thing I noticed is that the number of exons is almost twice larger then the number I see on the Wiki. (biostars.org)

We would also like to give a special shoutout to the individuals from Exon Software Solutions who leveled up their achievements at the ceremony. (exon.lk)

Diseases1

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