Exons
Alternative Splicing
A process whereby multiple RNA transcripts are generated from a single gene. Alternative splicing involves the splicing together of other possible sets of EXONS during the processing of some, but not all, transcripts of the gene. Thus a particular exon may be connected to any one of several alternative exons to form a mature RNA. The alternative forms of mature MESSENGER RNA produce PROTEIN ISOFORMS in which one part of the isoforms is common while the other parts are different.
Introns
Base Sequence
Molecular Sequence Data
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.
RNA Splicing
Amino Acid Sequence
RNA Splice Sites
Mutation
RNA, Messenger
RNA sequences that serve as templates for protein synthesis. Bacterial mRNAs are generally primary transcripts in that they do not require post-transcriptional processing. Eukaryotic mRNA is synthesized in the nucleus and must be exported to the cytoplasm for translation. Most eukaryotic mRNAs have a sequence of polyadenylic acid at the 3' end, referred to as the poly(A) tail. The function of this tail is not known for certain, but it may play a role in the export of mature mRNA from the nucleus as well as in helping stabilize some mRNA molecules by retarding their degradation in the cytoplasm.
Polymerase Chain Reaction
In vitro method for producing large amounts of specific DNA or RNA fragments of defined length and sequence from small amounts of short oligonucleotide flanking sequences (primers). The essential steps include thermal denaturation of the double-stranded target molecules, annealing of the primers to their complementary sequences, and extension of the annealed primers by enzymatic synthesis with DNA polymerase. The reaction is efficient, specific, and extremely sensitive. Uses for the reaction include disease diagnosis, detection of difficult-to-isolate pathogens, mutation analysis, genetic testing, DNA sequencing, and analyzing evolutionary relationships.
Cloning, Molecular
RNA Precursors
RNA transcripts of the DNA that are in some unfinished stage of post-transcriptional processing (RNA PROCESSING, POST-TRANSCRIPTIONAL) required for function. RNA precursors may undergo several steps of RNA SPLICING during which the phosphodiester bonds at exon-intron boundaries are cleaved and the introns are excised. Consequently a new bond is formed between the ends of the exons. Resulting mature RNAs can then be used; for example, mature mRNA (RNA, MESSENGER) is used as a template for protein production.
Pedigree
Polymorphism, Single-Stranded Conformational
Variation in a population's DNA sequence that is detected by determining alterations in the conformation of denatured DNA fragments. Denatured DNA fragments are allowed to renature under conditions that prevent the formation of double-stranded DNA and allow secondary structure to form in single stranded fragments. These fragments are then run through polyacrylamide gels to detect variations in the secondary structure that is manifested as an alteration in migration through the gels.
DNA
A deoxyribonucleotide polymer that is the primary genetic material of all cells. Eukaryotic and prokaryotic organisms normally contain DNA in a double-stranded state, yet several important biological processes transiently involve single-stranded regions. DNA, which consists of a polysugar-phosphate backbone possessing projections of purines (adenine and guanine) and pyrimidines (thymine and cytosine), forms a double helix that is held together by hydrogen bonds between these purines and pyrimidines (adenine to thymine and guanine to cytosine).
Protein Isoforms
DNA, Complementary
Sequence Homology, Nucleic Acid
Transcription, Genetic
Sequence Analysis, DNA
Genes
Point Mutation
Promoter Regions, Genetic
Restriction Mapping
DNA Primers
Chromosome Mapping
Codon, Nonsense
An amino acid-specifying codon that has been converted to a stop codon (CODON, TERMINATOR) by mutation. Its occurance is abnormal causing premature termination of protein translation and results in production of truncated and non-functional proteins. A nonsense mutation is one that converts an amino acid-specific codon to a stop codon.
Frameshift Mutation
A type of mutation in which a number of NUCLEOTIDES deleted from or inserted into a protein coding sequence is not divisible by three, thereby causing an alteration in the READING FRAMES of the entire coding sequence downstream of the mutation. These mutations may be induced by certain types of MUTAGENS or may occur spontaneously.
Sequence Alignment
The arrangement of two or more amino acid or base sequences from an organism or organisms in such a way as to align areas of the sequences sharing common properties. 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. This in turn can serve as a potential indicator of the genetic relatedness between the organisms.
Alleles
Mutation, Missense
Blotting, Southern
Dystrophin
A muscle protein localized in surface membranes which is the product of the Duchenne/Becker muscular dystrophy gene. Individuals with Duchenne muscular dystrophy usually lack dystrophin completely while those with Becker muscular dystrophy have dystrophin of an altered size. It shares features with other cytoskeletal proteins such as SPECTRIN and alpha-actinin but the precise function of dystrophin is not clear. One possible role might be to preserve the integrity and alignment of the plasma membrane to the myofibrils during muscle contraction and relaxation. MW 400 kDa.
Polymorphism, Genetic
The regular and simultaneous occurrence in a single interbreeding population of two or more discontinuous genotypes. The concept includes differences in genotypes ranging in size from a single nucleotide site (POLYMORPHISM, SINGLE NUCLEOTIDE) to large nucleotide sequences visible at a chromosomal level.
Reverse Transcriptase Polymerase Chain Reaction
Sequence Homology, Amino Acid
Genomic Library
Gene Deletion
Gene Expression Regulation
Tight binding of the 5' exon to domain I of a group II self-splicing intron requires completion of the intron active site. (1/14753)
Group II self-splicing requires the 5' exon to form base pairs with two stretches of intronic sequence (EBS1 and EBS2) which also bind the DNA target during retrotransposition of the intron. We have used dimethyl sulfate modification of bases to obtain footprints of the 5' exon on intron Pl.LSU/2 from the mitochondrion of the alga Pylaiella littoralis, as well as on truncated intron derivatives. Aside from the EBS sites, which are part of the same subdomain (ID) of ribozyme secondary structure, three distant adenines become either less or more sensitive to modification in the presence of the exon. Unexpectedly, one of these adenines in subdomain IC1 is footprinted only in the presence of the distal helix of domain V, which is involved in catalysis. While the loss of that footprint is accompanied by a 100-fold decrease in the affinity for the exon, both protection from modification and efficient binding can be restored by a separate domain V transcript, whose binding results in its own, concise footprint on domains I and III. Possible biological implications of the need for the group II active site to be complete in order to observe high-affinity binding of the 5' exon to domain I are discussed. (+info)A premature termination codon interferes with the nuclear function of an exon splicing enhancer in an open reading frame-dependent manner. (2/14753)
Premature translation termination codon (PTC)-mediated effects on nuclear RNA processing have been shown to be associated with a number of human genetic diseases; however, how these PTCs mediate such effects in the nucleus is unclear. A PTC at nucleotide (nt) 2018 that lies adjacent to the 5' element of a bipartite exon splicing enhancer within the NS2-specific exon of minute virus of mice P4 promoter-generated pre-mRNA caused a decrease in the accumulated levels of P4-generated R2 mRNA relative to P4-generated R1 mRNA, although the total accumulated levels of P4 product remained the same. This effect was seen in nuclear RNA and was independent of RNA stability. The 5' and 3' elements of the bipartite NS2-specific exon enhancer are redundant in function, and when the 2018 PTC was combined with a deletion of the 3' enhancer element, the exon was skipped in the majority of the viral P4-generated product. Such exon skipping in response to a PTC, but not a missense mutation at nt 2018, could be suppressed by frame shift mutations in either exon of NS2 which reopened the NS2 open reading frame, as well as by improvement of the upstream intron 3' splice site. These results suggest that a PTC can interfere with the function of an exon splicing enhancer in an open reading frame-dependent manner and that the PTC is recognized in the nucleus. (+info)Selection and characterization of pre-mRNA splicing enhancers: identification of novel SR protein-specific enhancer sequences. (3/14753)
Splicing enhancers are RNA sequences required for accurate splice site recognition and the control of alternative splicing. In this study, we used an in vitro selection procedure to identify and characterize novel RNA sequences capable of functioning as pre-mRNA splicing enhancers. Randomized 18-nucleotide RNA sequences were inserted downstream from a Drosophila doublesex pre-mRNA enhancer-dependent splicing substrate. Functional splicing enhancers were then selected by multiple rounds of in vitro splicing in nuclear extracts, reverse transcription, and selective PCR amplification of the spliced products. Characterization of the selected splicing enhancers revealed a highly heterogeneous population of sequences, but we identified six classes of recurring degenerate sequence motifs five to seven nucleotides in length including novel splicing enhancer sequence motifs. Analysis of selected splicing enhancer elements and other enhancers in S100 complementation assays led to the identification of individual enhancers capable of being activated by specific serine/arginine (SR)-rich splicing factors (SC35, 9G8, and SF2/ASF). In addition, a potent splicing enhancer sequence isolated in the selection specifically binds a 20-kDa SR protein. This enhancer sequence has a high level of sequence homology with a recently identified RNA-protein adduct that can be immunoprecipitated with an SRp20-specific antibody. We conclude that distinct classes of selected enhancers are activated by specific SR proteins, but there is considerable sequence degeneracy within each class. The results presented here, in conjunction with previous studies, reveal a remarkably broad spectrum of RNA sequences capable of binding specific SR proteins and/or functioning as SR-specific splicing enhancers. (+info)Substrate specificities of SR proteins in constitutive splicing are determined by their RNA recognition motifs and composite pre-mRNA exonic elements. (4/14753)
We report striking differences in the substrate specificities of two human SR proteins, SF2/ASF and SC35, in constitutive splicing. beta-Globin pre-mRNA (exons 1 and 2) is spliced indiscriminately with either SR protein. Human immunodeficiency virus tat pre-mRNA (exons 2 and 3) and immunoglobulin mu-chain (IgM) pre-mRNA (exons C3 and C4) are preferentially spliced with SF2/ASF and SC35, respectively. Using in vitro splicing with mutated or chimeric derivatives of the tat and IgM pre-mRNAs, we defined specific combinations of segments in the downstream exons, which mediate either positive or negative effects to confer SR protein specificity. A series of recombinant chimeric proteins consisting of domains of SF2/ASF and SC35 in various combinations was used to localize trans-acting domains responsible for substrate specificity. The RS domains of SF2/ASF and SC35 can be exchanged without effect on substrate specificity. The RNA recognition motifs (RRMs) of SF2/ASF are active only in the context of a two-RRM structure, and RRM2 has a dominant role in substrate specificity. In contrast, the single RRM of SC35 can function alone, but its substrate specificity can be influenced by the presence of an additional RRM. The RRMs behave as modules that, when present in different combinations, can have positive, neutral, or negative effects on splicing, depending upon the specific substrate. We conclude that SR protein-specific recognition of specific positive and negative pre-mRNA exonic elements via one or more RRMs is a crucial determinant of the substrate specificity of SR proteins in constitutive splicing. (+info)Identification of DNA polymorphisms associated with the V type alpha1-antitrypsin gene. (5/14753)
alpha1-Antitrypsin (alpha1-AT) is a highly polymorphic protein. The V allele of alpha1-AT has been shown to be associated with focal glomerulosclerosis (FGS) in Negroid and mixed race South African patients. To identify mutations and polymorphisms in the gene for the V allele of alpha1-AT in five South African patients with FGS nephrotic syndrome DNA sequence analysis and restriction fragment length polymorphisms of the coding exons were carried out. Four of the patients were heterozygous for the BstEII RFLP in exon III [M1(Val213)(Ala213)] and one patient was a M1(Ala213) homozygote. The mutation for the V allele was identified in exon II as Gly-148 (GGG)-->Arg (AGG) and in all patients was associated with a silent mutation at position 158 (AAC-->AAT). The patient who was homozygous for (Ala213) also had a silent mutation at position 256 in exon III (GAT-->GAC) which was not present in any of the other four patients. Although the V allele of alpha1-AT is not associated with severe plasma deficiency, it may be in linkage disequilibrium with other genes on chromosome 14 that predispose to FGS. Furthermore, the associated silent mutation at position 158 and the Ala213 polymorphism are of interest, as these could represent an evolutionary intermediate between the M1(Ala213) and M1(Val213) subtypes. (+info)Promoter and exon-intron structure of the protein kinase C gene from the marine sponge Geodia cydonium: evolutionary considerations and promoter activity. (6/14753)
We report the gene structure of a key signaling molecule from a marine sponge, Geodia cydonium. The selected gene, which codes for a classical protein kinase C (cPKC), comprises 13 exons and 12 introns; the introns are, in contrast to those found in cPKC from higher Metazoa, small in size ranging from 93 nt to 359 nt. The complete gene has a length of 4229 nt and contains exons which encode the characteristic putative regulatory and catalytic domains of metazoan cPKCs. While in the regulatory domain only one intron is in phase 0, in the catalytic domain most introns are phase 0 introns, suggesting that the latter only rarely undergo module duplication. The 5'-flanking sequence of the sponge cPKC gene contains a TATA-box like motif which is located 35-26 nt upstream from the start of the longest sequenced cDNA. This 5'-flanking sequence was analyzed for promoter activity. The longest fragment (538 nt) was able to drive the expression of luciferase in transient transfections of NIH 3T3 fibroblasts; the strong activity of the sponge promoter was found to be half the one displayed by the SV40 reference promoter. Deletion analysis demonstrates that the AP4 site and the GC box which is most adjacent to the TATA box are the crucial elements for maximal promoter activity. The activity of the promoter is not changed in 3T3 cells which are kept serum starved or in the presence of a phorbol ester. In conclusion, these data present the phylogenetically oldest cPKC gene which contains in the 5'-flanking region a promoter functional in the heterologous mammalian cell system. (+info)Expression of novel alternatively spliced isoforms of the oct-1 transcription factor. (7/14753)
Analysis of the alternatively spliced isoforms of the human and mouse oct-1 genes, combined with their exon-intron structure, show a high level of evolutionary conservation between these two species. The differential expression of several oct-1 isoforms was examined by reverse transcription-polymerase chain reaction performed on the 3' region of the murine oct-1 cDNA. Variations in the relative levels and patterns of expression of the isoforms were found among different tissues. Three novel isoforms originating from the 3'-distal region of oct-1, were isolated and sequenced: Two were derived from testis, and one from myeloma cells. Splicing out of different exons as revealed in the structure of these isoforms results in reading frameshifts that presumably lead to the expression of shortened Oct-1 proteins, with distinct C-terminal tails. Altogether, six out of the eight known murine oct-1 isoforms may have distinct C-termini, implying that these multiple tails have different functional roles in cellular differentiation and physiology. (+info)The alphaE-catenin gene (CTNNA1) acts as an invasion-suppressor gene in human colon cancer cells. (8/14753)
The acquisition of invasiveness is a crucial step in the malignant progression of cancer. In cancers of the colon and of other organs the E-cadherin/catenin complex, which is implicated in homotypic cell-cell adhesion as well as in signal transduction, serves as a powerful inhibitor of invasion. We show here that one allele of the alphaE-catenin (CTNNA1) gene is mutated in the human colon cancer cell family HCT-8, which is identical to HCT-15, DLD-1 and HRT-18. Genetic instability, due to mutations in the HMSH6 (also called GTBP) mismatch repair gene, results in the spontaneous occurrence of invasive variants, all carrying either a mutation or exon skipping in the second alphaE-catenin allele. The alphaE-catenin gene is therefore, an invasion-suppressor gene in accordance with the two-hit model of Knudsen for tumour-suppressor genes. (+info)
Exon
Common incorrect uses of the term exon are that 'exons code for protein', or 'exons code for amino-acids' or 'exons are ... The first exon of a 'trapped' gene splices into the exon that is contained in the insertional DNA. This new exon contains the ... The average exon encoded 30-36 amino acids. While the longest exon in the human genome is 11555 bp long, several exons have ... Exon trapping or 'gene trapping' is a molecular biology technique that exploits the existence of the intron-exon splicing to ...
Exon (disambiguation)
Look up exon in Wiktionary, the free dictionary. Exon may refer to: Exon, a region of DNA that is represented in the mature ... James Exon (1921-2005), American politician Nat Exon (born 1992), Australian rules footballer Exon is a rank for an officer in ... an RNA degrading enzyme Exoniensis or Exon., the Post-Nominal Letters for alumni / degrees from the University of Exeter Exon ... a brand of fuel sold by ExxonMobil This disambiguation page lists articles associated with the title Exon. If an internal link ...
Exon skipping
Multiple exon skipping has successfully been carried out using a combination of AONs that target multiple exons. Exon skipping ... Another exon-skipping Morpholino, golodirsen (Vyondys 53) (targeting dystrophin exon 53), was approved in the United States in ... Genes are the genetic instructions for creating a protein, and are composed of introns and exons. Exons are the sections of DNA ... to induce exon skipping. The AON binds to the mutated exon, so that when the gene is then translated from the mature mRNA, it ...
Arthur Exon
In 1947, Exon became a member of the U.S. Air Force when it became a separate branch of the military. Exon was assigned to "Air ... In 1938, Exon returned to Fairfax, becoming principal of the junior high school. In 1942, Exon entered the US Army and by March ... Exon was captured by Germans and held as a prisoner of war until June 1945. Exon was awarded the Distinguished Service Cross " ... Exon was born in 1916 in Geddes, South Dakota. Exon attended high school in Fairfax before studying at Southern State Teachers ...
Nat Exon
Exon was born in 1992. She was playing for the Darebin Falcons when she was drafted. Exon was recruited by Carlton as a rookie ... Exon's brother, Ryan, plays for the Coburg Lions in the mens VFL. On 25 May 2017, Exon was, along with Bella Ayre, traded to ... Nat Exon's profile on the official website of the St Kilda Football Club Nat Exon at AustralianFootball.com v t e (Articles ... In April 2019, Exon joined expansion club St Kilda along with fellow Brisbane player Kate McCarthy. It was revealed Exon had ...
Exon shuffling
... or the same exon can be duplicated, to create a new exon-intron structure. There are different mechanisms through which exon ... Exon shuffling is a molecular mechanism for the formation of new genes. It is a process through which two or more exons from ... Exon shuffling follows certain splice frame rules. Introns can interrupt the reading frame of a gene by inserting a sequence ... Exon shuffling was first introduced in 1978 when Walter Gilbert discovered that the existence of introns could play a major ...
Exon trapping
... is a molecular biology technique to identify potential exons in a fragment of eukaryote DNA of unknown intron- ... The genomic fragment is inserted into the intron of a 'splicing vector' consisting of a known exon - intron - exon sequence of ... thereby identifying the appropriate exon-intron splice sites. Duyk, G. M, S. W. Kim, R. M Myers, and D. R Cox. 1990. "Exon ... If the fragment does not contain exons (i.e., consists solely of intron DNA), it will be spliced out together with the vector's ...
Exon junction complex
An exon junction complex (EJC) is a protein complex which forms on a pre-messenger RNA strand at the junction of two exons ... Le Hir H, Gatfield D, Izaurralde E, Moore MJ (2001). "The exon-exon junction complex provides a binding platform for factors ... Lykke-Andersen, J.; Shu, M.-D.; Steitz, J. A. (2001). "Communication of the Position of Exon-Exon Junctions to the mRNA ... where two exons are joined), when the lariat has formed and the exons are ligated together. The binding of the EJC to the mRNA ...
Tandem exon duplication
... is defined as duplication of exons within the same gene to give rise to the subsequent exon. A complete ... 1,578 of these unannotated exons contained stop codons thus not considered potential exons. 35.1% of the unannotated exons were ... Analysis of the intronic region has produced further 4,660 unidentified duplicated exons referred to as unannotated exons. ... Gene duplication Letunic I, Copley RR, Bork P (Jun 2002). "Common exon duplication in animals and its role in alternative ...
J. James Exon
The Exon Library Exon's Congressional biography New York Times article on Exon's death Los Angeles Times article on Exon's ... Exon was Chair of the Nebraska Democratic Party in 1970 when he decided to run for Governor. Exon's first bid for public office ... Exon later claimed that he received an unspecified settlement from Exxon in exchange for renaming his business the J.J. Exon ... In 1988, Exon took 10 vacations paid for by lobbying groups. Exon helped to write and secure support for a spending reduction ...
Exon-Florio Amendment
The Exon-Florio Amendment 50 U.S.C. app 2170 is a law that was enacted by the United States Congress in 1988 to review foreign ... The amendment was sponsored by Senator J. James Exon and Representative James J. Florio. The amendment was proposed over ...
Philip of Exon
... was Archdeacon of Barnstaple until 1279. "Memorials of Barnstaple; being an attempt to supply the want of a ...
Exon-intron database
The Exon-Intron Database (EID) is a database of spliced mRNA sequences. Alternative splicing Exon Intron Saxonov, S; Daizadeh I ... Fedorov A; Gilbert W (Jan 2000). "EID: the Exon-Intron Database-an exhaustive database of protein-coding intron-containing ...
Trans-Spliced Exon Coupled RNA End Determination
... (TEC-RED) is a transcriptomic technique that, like SAGE, allows for the ...
Netrin receptor DCC
The DCC gene is located at 18q21.3, and has a total of 57 possible exons and 43 possible introns. This theoretically results in ... Nigro JM, Cho KR, Fearon ER, Kern SE, Ruppert JM, Oliner JD, Kinzler KW, Vogelstein B (1991). "Scrambled exons". Cell. 64 (3): ...
TMEM125
... comprises four exons. Five TMEM125 promoters were identified by Genomatix Gene2Promoter. The primary promoter (NM_ ...
CFAP206
... it has 13 exons and 12 coding exons; the translation length is 622 residues The second protein coding transcript in human is ... the start codon is at the second exon of the mRNA and this indicate the first exon is spliced during the modification. In ... it contains 7 exons and only 6 exons are protein coding; the translation length is 252 residues Two-hybrid experiments revealed ... It contains 12 exons. The genomic DNA is 54,407 base pairs long, while the longest mRNA that it produces is 2,215 bp long. This ...
HLA-A
The protein coded for by the HLA-A gene is 365 amino acids long and weighs roughly 41,000 Daltons (Da). It contains 8 exons. ...
Helicase, POLQ-like
It contains twenty exons. Helicase Q's principal role is in the DNA repair. Helicase Q was shown to play a role in the repair ...
C17orf75
... has 10 exons. C17orf75 has 4 transcript isoforms: C17orf75 and 3 predicted isoforms which are C17orf75 transcript ...
ACOT1
It contains 7 exons. The protein encoded by this gene contains 410 amino acids, and forms a homodimer with another chain. The ...
TEX9
... is located at 15q21.3 and has 18 exons. However, some exons overlap; therefore, there are only 13 distinguishable exons in ...
Uncharacterized protein C15orf32
It contains 3 exons. Two isoforms of C15orf32 exist. The longer transcript, known as transcript variant 2 on NCBI, is 1,764 ... Three SNPs within C15orf32, including rs1455773 in exon 1 which causes a missense mutation from alanine to threonine at ...
SHLD1
It contains 11 exons. Its aliases are RINN3 and SHLD1. C20orf196 produces 9 different mRNAs, with 7 alternatively spliced ... The mRNAs differ by the truncation of the 5' end, truncation of the 3' end, presence or absence of 2 cassette exons, and ... There are 3 probable alternative promoters, 3 non-overlapping alternative last exons, and 2 alternative polyadenylation sites. ... overlapping exons with different boundaries. C20orf196 has six splice isoforms. The promoter region is within bases 5749286 to ...
Pseudoachondroplasia
COMP contains 19 exons. The cartilage oligomeric matrix protein is 757 aa (OMIM 2008). COMP protein is found in the ...
Basic leucine zipper and W2 domain-containing protein 2
There are 12 exons. There are two known isoforms of BZW2. Isoform 1 is 419 amino acids long and is the most abundant form. ... Isoform 2 is 225 amino acids, containing only 11 exons and a shorter N-terminus. The coded protein is 419 amino acids long and ...
ACOT11
It contains 18 exons. The protein encoded by this gene contains 258 amino acids, and forms a homodimer with another chain. Its ...
GLS2
It contains 19 exons. GLS2 is a part of the glutaminase family. The protein encoded by this gene is a mitochondrial phosphate- ...
H3K36me3
... might define exons. Nucleosomes in the exons have more histone modifications such as H3K79, H4K20, and especially ...
Jrk
It has 9 exons. The transcript of the gene is about 5000kB long, as determined through utilization of northern blot techniques ...
Mutations primarily alter the inclusion of alternatively spliced exons | eLife
Deep mutagenesis reveals that mutations rarely alter the inclusion of highly-included exons. ... exon_1nt, rnd_exon_2nt, rnd_exon_3nt, rnd_exon_5nt, aggr_exon. The effect of a mutation was calculated by subtracting ... PSMD14 exon 11) was predicted using the rescaled distribution of mutation effects in FAS exon 6, RON exon 11 and WT1 exon 5 (99 ... one for FAS exon 6, one for RON exon 11 and four for WT1 exon 5 - WT1 exon five version B was not included since it ...
Noisy splicing, more than expression regulation, explains why some exons are subject to nonsense-mediated mRNA decay | BMC...
However, nonsense-mediated decay-specific exons for which distant orthologous exons can be found tend to have been under ... That some exons have premature termination codons at fixation is paradoxical: why make a transcript if it is only to be ... We conclude that for recently evolved exons the noisy splicing model is the better explanation of their properties, while for ... Several lines of evidence suggested that the noisy splicing model has considerable relevance: 1) exons that are uniquely found ...
Exon C3 - Herz GmbH Kunststoff & Wärmetechnologie
EdgeR diffSpliceDGE: Obtaining exon-level counts and normalisation step
how to obtain exon level counts. One way to obtain exon level counts is to run featureCounts. of the Rsubread. package with ... Is there a way to extract exon-level counts from these files? In case it matters Im analysing data from an exon skipping ... edger normalization differential exon usage splicing • 1.5k views ADD COMMENT • link updated 2.7 years ago by Yunshun Chen & ... The exon information is still preserved in y.all$genes. .. I dont see anything wrong with the design. There are 6 RNA-seq ...
Exon Publications
Open access books editors of Exon Publications width=600 height=596,,/p,. Exon Publications. en-US. Exon Publications. ,p, ... p,Open access books published by Exon Publications, Brisbane, Australia, are indexed in NCBI/NIH/NLM Bookshelf, ,a href=https ... Exon Publications provides multiple options for publication. Authors can publish chapters in the book series ,em,Advancements ... exonpublications.com/index.php/exon/pubmed-indexing,PubMed,/a,, ,a href=https://exonpublications.com/index.php/exon/europe- ...
Exon ICT Group
Introns Vs Exons: What's The Difference? » Differencess
... you probably dont know the difference between introns and exons. In this article, well explore the basics of these two gene ... Exons are the sections of DNA that carry genetic information. Most genes have one or two exons, but some genes have more. Exons ... What are Exons?. Exons are the segments of DNA that make up a gene. Introns are the segments of DNA that dont make up a gene. ... Exons are the sections of DNA that make up a gene.. Most genes have a mix of intron and exon usage. Intron usage tends to be ...
c-KIT gene Mutations (4 Exons) - MolQMET exon 14 skipping Archives - Inspire
What Are Patients and Caregivers Talking About? Lung Cancer Biomarkers By Kathleen Hoffman, PhD, MSPH Since the FDA approved the first targeted treatment for NSCLC in 2003, treatment decisions for NSCLC are increasingly made based on individual genomics.1,2 There are now 20 distinct biomarkers that serve as identification points differentiating cancer cells ...
Exon : Details on the Discord Server
Epigenetic regulation of CDH1 exon 8 alternative splicing in gastric cancer | BMC Cancer | Full Text
In our previous work, we reported a nonfunctional CDH1 transcript that lacks the final 83 base pairs of exon 8 (1054del83). In ... H3K36me3 correlates with increased skipping of the final 83 base pairs of CDH1 exon 8. Histone acetylation was involved in the ... SiRNA-mediated knockdown of SETD2 (The specific methyltransferase of H3K36) decreased exclusion of exon 8, suggesting that the ... Treatment with TSA preferentially expressed the correctly spliced transcript and not the exon 8 skipped aberrant transcripts, ...
Exon skipping for point mutations - Exon skipping
Explanation of the exon skipping technique for point mutations in DMD patients ... exon 42 and exon 44 do not fit). However, a deletion of exon 43 and exon 44 is in-frame (321 nucleotides, divisible by 3). Thus ... Figure 1. Single exon skipping for point mutations. If the small mutation is present in an exon that contains a number of ... cells from a patient with the deletion of a single nucleotide in exon 43 with AONs targeting exon 43 and AONs targeting exon 44 ...
Post-transcriptional exon shuffling events in humans can be evolutionarily conserved and abundant - ePrints - Newcastle...
Finally, we use real-time PCR to compare the abundance of PTES exon junctions relative to canonical exon junctions within the ... Post-transcriptional exon shuffling events in humans can be evolutionarily conserved and abundant. Lookup NU author(s): Haya AL ... PTES exon junctions are present at ,0.01% to ,90% of the levels of canonical junctions, with transcripts from MAN1A2, PHC3, ... In silico analyses have established that transcripts from some genes can be processed into RNAs with rearranged exon order ...
Refubium - Exon skipping as a therapeutic strategy in dysferlinopathy
Exon skipping was detected at the RNA level only in C2C12 cells. The thesis investigates also if dysferlin without exons 37 or ... Exon skipping as a therapeutic strategy in dysferlinopathy. Haupttitel: Exon skipping as a therapeutic strategy in ... None of these AONs was able to evoke detectable skipping of exon 38 or both exon 37 and 38 at the RNA level. As an alternative ... Das Dysferlin ohne Exon 37 und ohne die beiden Exons 37 und 38 verfügt über die gleiche Membranreparaturfähigkeit wie das ...
Molecular Inversion Probe-Based Sequencing of |i|USH2A|/i| Exons and Splice Sites as a Cost-Effective Screening Tool in USH2...
Instagram Ads Masterclass: Create Instagram Ads that Sell | Diego Davila | Skillshare
GeneLoc Integrated Map for Chromosome 12: Exon structure for RPL37AP9
CB-AB-EX-ON-2016-11 | Infernal Masquerade Photography Vault
Recenze: Annemieke Aartsma-Rus (ed.): Exon Skipping: Methods and Protocols
| Chemické listy
Rare, low-frequency, and common variants in the protein-coding sequence of biological candidate genes from GWASs contribute to...
Occupational Fatalities Associated With 2,4-Dichlorophenol
(2,4-DCP) Exposure, 1980--1998
CCDS Report for Consensus CDS
Article - Billing and Coding: MolDX: Molecular Diagnostic Tests (MDT) (A57772)
U.S. Senate: U.S. Senate Roll Call Votes 102nd Congress - 2nd Session
The genomic structure of murine CD33 reveals multiple exons in its cytoplasmic tail and several potential 5' regulatory...
Association of nuclear matrix antigens with exon-containing splicing complexes. | Journal of Cell Biology | Rockefeller...
Association of nuclear matrix antigens with exon-containing splicing complexes. B J Blencowe, B J Blencowe ... B J Blencowe, J A Nickerson, R Issner, S Penman, P A Sharp; Association of nuclear matrix antigens with exon-containing ... The anti-NM mAbs efficiently immunoprecipitate the exon product complex but not complexes containing the lariat product after ... The Acute Myeloid Leukemia-Associated Protein, Dek, Forms a Splicing-Dependent Interaction with Exon-Product Complexes ...
Born on August 9th
HLA-G exon 8 polymorphism in type 1 diabetes among north Indians<...
HLA-G exon 8 polymorphism in type 1 diabetes among north Indians. Tissue Antigens. 2012 Jul;80(1):102. Epub 2012 Jun 1. doi: ... HLA-G exon 8 polymorphism in type 1 diabetes among north Indians. In: Tissue Antigens. 2012 ; Vol. 80, No. 1. pp. 102. ... HLA-G exon 8 polymorphism in type 1 diabetes among north Indians. / Mourya, Manish; Tandon, Nikhil; Sood, Prashant et al. ... Mourya, M, Tandon, N, Sood, P, Saxena, A, Coshic, P, Mehra, NK & Kanga, U 2012, HLA-G exon 8 polymorphism in type 1 diabetes ...
Lack of association of TPH2 exon XI polymorphisms with major depression and treatment resistance [3]<...
Lack of association of TPH2 exon XI polymorphisms with major depression and treatment resistance [3]. / Garriock, H. A.; Allen ... Lack of association of TPH2 exon XI polymorphisms with major depression and treatment resistance [3]. In: Molecular Psychiatry ... Lack of association of TPH2 exon XI polymorphisms with major depression and treatment resistance [3]. Molecular Psychiatry. ... Lack of association of TPH2 exon XI polymorphisms with major depression and treatment resistance [3]. ...
Cancer exosomes induce tumor innervation | Nature Communications
... exon 4 of RAB27B, and a sequence of exon 3 shared by RAB27A and B were co-transfected. PCR revealed a heterozygous, truncated ... end of the deletion in exon 1 occurs just after the signal peptide while the 3′ end of the deletion in exon 5 is within the ... The sequence data shows that Exons 2-4 are deleted; these exons comprise the majority of the extracellular domain of EphrinB1 ( ... One strategy employed simultaneous double-targeting to remove a large portion of gDNA spanning exons 1-5 (as in ref. 68) and ...
Mutations10
- Genetic analyses and systematic mutagenesis have revealed that synonymous, non-synonymous and intronic mutations frequently alter the inclusion levels of alternatively spliced exons, consistent with the concept that altered splicing might be a common mechanism by which mutations cause disease. (elifesciences.org)
- Here, by performing deep mutagenesis of highly-included exons and by analysing the association between genome sequence variation and exon inclusion across the transcriptome, we report that mutations only very rarely alter the inclusion of highly-included exons. (elifesciences.org)
- Therefore, mutations that affect splicing are not evenly distributed across primary transcripts but are focussed in and around alternatively spliced exons with intermediate inclusion levels. (elifesciences.org)
- To evaluate how often random mutations alter the inclusion of exons, several groups have recently subjected exons in mini-gene constructs to deep mutational scanning (DMS) ( Kinney and McCandlish, 2019 ). (elifesciences.org)
- In these DMS experiments, the effects of hundreds or thousands of mutations in or around an exon are quantified in parallel by selection and sequencing. (elifesciences.org)
- further revealed that mutations in ~80% of intronic positions flanking RON exon 11 also affect its inclusion. (elifesciences.org)
- The main difference between these two effects is that mutations caused by intron usage generally don't have as big an impact on the organism as mutations caused by exon usage. (differencess.com)
- Mutations in exons 5-8 of the p53 tumor suppressor gene were determined by direct DNA sequence analysis. (cdc.gov)
- No mutations were found in exons 5-8 of the p53 gene in any of the mesothelioma tissue samples analyzed. (cdc.gov)
- In Kuwait, no precise data are the only exons where mutations have been available, although some reports have been previously reported [ 5 ]. (who.int)
Gene15
- In case it matters I'm analysing data from an exon skipping experiment and so will be looking at differential splicing for our gene of interest as well as any off-target effects. (bioconductor.org)
- The standard filtering and normalization steps for the gene-level analysis can also be applied to the exon-level. (bioconductor.org)
- Exons are the segments of DNA that make up a gene. (differencess.com)
- Exons are the parts of a gene that code for the proteins that a gene produces. (differencess.com)
- They serve as segments between protein-coding regions (exons) and are thought to play a role in regulating gene expression. (differencess.com)
- Exons are the segments of DNA that make up the bulk of a gene and are typically found in messenger RNA (mRNA). (differencess.com)
- How do intron and exon usage affect the function of the gene? (differencess.com)
- Introns and exons are found in every gene, but why are they important? (differencess.com)
- A significant decrease in acetylation for histones H3 and H4K16Ac in an internal region of the CDH1 gene surrounding the alternative exon 8 were detected in GC cell lines. (biomedcentral.com)
- C in the exon 38 of the dysferlin gene. (fu-berlin.de)
- The peptide-binding groove binds killer-cell immunoglobulin-like receptor exons, while the polymorphisms reside endogenously derived peptides, which in (KIR) molecules on the surfaces of natural in gene regions that encode the peptide- turn are recognised by the TCR on CD8+ killer (NK) cel s and the recognition and binding groove. (who.int)
- We report 8 patients from 7 Jordanian families, 6 of whom underwent genetic testing and were found to have a 12 bp (155-166 del) deletion within the tubulin-specific chaperone E ( TBCE gene) in exon 3 at 1q42-43. (who.int)
- All affected persons had homozygous deletion of 12 bp (155-166del) in exon 3 of the TBCE gene. (who.int)
- Exons 2 (first coding exon), 3 (second cod- and Kuwait: the incidence in Saudi Ara- ing exon) and 12 of the TBCE gene were bia varies from 1:40 000 to 1:100 000 live chosen for the initial screening as they were births [ 6 ]. (who.int)
- 22. Hayashi SI, Kawajiri K, Nakachi K, Watanabe J. PCR detection of an A/G polymorphism within exon 7 of the CYP1A1 gene. (bvsalud.org)
Sequences5
- Apart from the splice sites, pre-mRNAs contain exonic and intronic sequences that interact with different splicing factors to regulate how often each exon is included in the final transcript ( Wang and Burge, 2008 ). (elifesciences.org)
- Exons, on the other hand, are the protein-coding sequences that make up the majority of the genome. (differencess.com)
- Twelve antisense sequences targeting exon 38 were cloned into the U7 snRNA backbone. (fu-berlin.de)
- We estimated selection pressures in tat exon 1 using the mixed-effects model of evolution with 672 viral sequences generated from 20 patients infected with HIV-1 subtype C ( HIV -1C) over 500 days postseroconversion. (bvsalud.org)
- Surprisingly, all three of these mAbs preferentially immunoprecipitate splicing complexes containing exon sequences. (silverchair.com)
Single-nucleotide1
- Treating cultured cells from a patient with the deletion of a single nucleotide in exon 43 with AONs targeting exon 43 and AONs targeting exon 44 indeed resulted in the generation of dystrophin. (exonskipping.nl)
Genomic structure1
- In silico analyses have established that transcripts from some genes can be processed into RNAs with rearranged exon order relative to genomic structure (post-transcriptional exon shuffling, or PTES). (ncl.ac.uk)
Skipping14
- SiRNA-mediated knockdown of SETD2 (The specific methyltransferase of H3K36) decreased exclusion of exon 8, suggesting that the presence of this mark correlates with increased skipping of the final 83 base pairs of CDH1 exon 8. (biomedcentral.com)
- H3K36me3 correlates with increased skipping of the final 83 base pairs of CDH1 exon 8. (biomedcentral.com)
- Either way, if the mutation is present in an in-frame exon, such as exon 49 that contains 102 nucleotides (divisible by 3), the mutation can be bypassed by skipping said exon (Figure 1). (exonskipping.nl)
- If the small mutation is present in an exon that contains a number of nucleotides not divisible by 3 ( e.g. exon 43 contains 173 nucleotides), skipping of the mutated exon will bypass mutation, but cause a disruption of the reading frame at the same time ( i.e. exon 42 and exon 44 do not fit). (exonskipping.nl)
- Thus by inducing the combined skipping of both exon 43 and exon 44 the mutation can be bypassed, while the reading frame is maintained (Figure 2). (exonskipping.nl)
- Antisense oligonucleotides and U7 snRNAs delivered by an adeno-associated viral vector were used as tools to trigger exon skipping in vitro and in vivo. (fu-berlin.de)
- Out of thirteen AONs only five demonstrated low level of skipping exon 38. (fu-berlin.de)
- None of these AONs was able to evoke detectable skipping of exon 38 or both exon 37 and 38 at the RNA level. (fu-berlin.de)
- The exon skipping activity of these three constructs was also verified in MMex38 dysferlin deficient mice. (fu-berlin.de)
- Two constructs evoked minor exon skipping detectable only at the RNA level. (fu-berlin.de)
- Exon skipping was detected at the RNA level only in C2C12 cells. (fu-berlin.de)
- Antisense- Oligonukleotide und U7 snRNAs, die durch einen adeno-assoziierten viralen Vektor geliefert wurden, sind Werkzeuge, die für das Exon Skipping in vitro und in vivo eingesetzt wurden. (fu-berlin.de)
- Therapeutic exon skipping for dysferlinopathies? (bvsalud.org)
- NICE is unable to make a recommendation on capmatinib (Tabrecta) for treating advanced non-small-cell lung cancer with MET exon 14 skipping in adults. (bvsalud.org)
Transcripts2
- Treatment with TSA preferentially expressed the correctly spliced transcript and not the exon 8 skipped aberrant transcripts, showing that histone acetylation was involved in the splicing regulation. (biomedcentral.com)
- Finally, we use real-time PCR to compare the abundance of PTES exon junctions relative to canonical exon junctions within the transcripts from seven genes. (ncl.ac.uk)
TBCE1
- les analyses génétiques réalisées sur six d'entre eux ont révélé une délétion de 12 bp (155-166 del) dans l'exon 3 localisé en 1q42-43 dans le gène TBCE codant la protéine chaperon E spécifique de la tubuline. (who.int)
Intron10
- To carry out the splicing reaction, exon-intron boundaries in the pre-mRNA must be correctly identified. (elifesciences.org)
- The differences between intron and exon usage have significant implications for disease pathogenesis and treatment. (differencess.com)
- Most genes have a mix of intron and exon usage. (differencess.com)
- Intron usage tends to be more common inrier in the genome, while exon usage is more common towards the end of the genome. (differencess.com)
- Why are researchers interested in intron and exon usage? (differencess.com)
- Scientists are interested in intron and exon usage because they can use this information to learn more about how genes work and how diseases develop. (differencess.com)
- Scientists study intron and exon usage to better understand how genes function and how diseases develop. (differencess.com)
- They also use intron and exon usage as markers for genetic disorders. (differencess.com)
- What implications do intron and exon usage have for human health? (differencess.com)
- Thirteen AONs masking exon 37, 38 and intron 37-38 of human dysferlin pre-mRNA were designed. (fu-berlin.de)
Genome2
- Introns and exons are two types of genetic code found in the human genome. (differencess.com)
- In this study, we addressed this issue by deep exon sequencing and large-scale genotyping of 25 biological candidate genes located within RA risk loci discovered by genome-wide association studies (GWASs). (nih.gov)
Skip1
- Three out of twelve U7 snRNAs were able to skip exon 37 and 38 simultaneously. (fu-berlin.de)
Genes2
- Most genes have one or two exons, but some genes have more. (differencess.com)
- Introns serve as a break between genes, while exons are the sections of DNA that make up the protein-coding portions of genes. (differencess.com)
Methods1
- Methods: We assessed DNA methylation at three CpG sites in the NOS2 exon 1 from blood from 201 welders. (cdc.gov)
Methylation2
- All the cell lines showed significant methylation pattern at the CpG sites of CDH1 exon 8. (biomedcentral.com)
- Given these observations, we probed the role of histone epigenetic modifications as well as DNA methylation in pre-mRNA alternative splicing of CDH1 exon 8. (biomedcentral.com)
Splice1
- The in silico analysis provided numerous exonic splice enhancers (ESEs) as possible targets and showed that exon 37 and 38 are in close proximity suggesting that they could be removed simultaneously. (fu-berlin.de)
Deletion1
- However, a deletion of exon 43 and exon 44 is in-frame (321 nucleotides, divisible by 3). (exonskipping.nl)
Patients2
- 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)
Data2
- I'm looking for some help when analysing RNA-Seq data for differential exon usage/splicing. (bioconductor.org)
- How, if at all, should the exon level count data be normalised prior to analysis? (bioconductor.org)
Selection1
- tat exon 1 residues 3, 4, 21, 24, 29, 39, and 68 were under positive selection, and we established that specific amino acid signature patterns were apparent in primary HIV -1C infection compared with chronic infection . (bvsalud.org)
Multiple2
- As these are exon-level counts, I'd expect the same ID appearing on multiple rows. (bioconductor.org)
- Exon Publications provides multiple options for publication. (exonpublications.com)
Primary1
- tat Exon 1 exhibits functional diversity during HIV-1 subtype C primary infection. (bvsalud.org)
Level2
- Is there a way to extract exon-level counts from these files? (bioconductor.org)
- I've read in my BAM files and successfully generated exon level counts as you described and as per the manual. (bioconductor.org)
Association1
- Association of nuclear matrix antigens with exon-containing splicing complexes. (silverchair.com)
Type1
- Using Oligo software, Kuwait identified as KCS type 1 showed version 3.4, 3 polymerase chain reaction that they fulfilled the criteria for SSS, and (PCR) primer sets to amplify exons 2, 3, and might be considered as such. (who.int)
Carry1
- Exons are the sections of DNA that carry genetic information. (differencess.com)
Final1
- In our previous work, we reported a nonfunctional CDH1 transcript that lacks the final 83 base pairs of exon 8 (1054 del 83). (biomedcentral.com)
Product1
- The anti-NM mAbs efficiently immunoprecipitate the exon product complex but not complexes containing the lariat product after the second step of splicing. (silverchair.com)
