The parts of a transcript of a split GENE remaining after the INTRONS are removed. They are spliced together to become a MESSENGER RNA or other functional RNA.
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.
Sequences of DNA in the genes that are located between the EXONS. They are transcribed along with the exons but are removed from the primary gene transcript by RNA SPLICING to leave mature RNA. Some introns code for separate genes.
The sequence of PURINES and PYRIMIDINES in nucleic acids and polynucleotides. It is also called nucleotide sequence.
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.
The ultimate exclusion of nonsense sequences or intervening sequences (introns) before the final RNA transcript is sent to the cytoplasm.
The order of amino acids as they occur in a polypeptide chain. This is referred to as the primary structure of proteins. It is of fundamental importance in determining PROTEIN CONFORMATION.
Nucleotide sequences located at the ends of EXONS and recognized in pre-messenger RNA by SPLICEOSOMES. They are joined during the RNA SPLICING reaction, forming the junctions between exons.
Any detectable and heritable change in the genetic material that causes a change in the GENOTYPE and which is transmitted to daughter cells and to succeeding generations.
Biochemical identification of mutational changes in a nucleotide sequence.
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.
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.
The insertion of recombinant DNA molecules from prokaryotic and/or eukaryotic sources into a replicating vehicle, such as a plasmid or virus vector, and the introduction of the resultant hybrid molecules into recipient cells without altering the viability of those cells.
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.
The record of descent or ancestry, particularly of a particular condition or trait, indicating individual family members, their relationships, and their status with respect to the trait or condition.
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.
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).
Different forms of a protein that may be produced from different GENES, or from the same gene by ALTERNATIVE SPLICING.
Single-stranded complementary DNA synthesized from an RNA template by the action of RNA-dependent DNA polymerase. cDNA (i.e., complementary DNA, not circular DNA, not C-DNA) is used in a variety of molecular cloning experiments as well as serving as a specific hybridization probe.
Deletion of sequences of nucleic acids from the genetic material of an individual.
The sequential correspondence of nucleotides in one nucleic acid molecule with those of another nucleic acid molecule. Sequence homology is an indication of the genetic relatedness of different organisms and gene function.
The biosynthesis of RNA carried out on a template of DNA. The biosynthesis of DNA from an RNA template is called REVERSE TRANSCRIPTION.
A multistage process that includes cloning, physical mapping, subcloning, determination of the DNA SEQUENCE, and information analysis.
A category of nucleic acid sequences that function as units of heredity and which code for the basic instructions for the development, reproduction, and maintenance of organisms.
A mutation caused by the substitution of one nucleotide for another. This results in the DNA molecule having a change in a single base pair.
DNA sequences which are recognized (directly or indirectly) and bound by a DNA-dependent RNA polymerase during the initiation of transcription. Highly conserved sequences within the promoter include the Pribnow box in bacteria and the TATA BOX in eukaryotes.
Use of restriction endonucleases to analyze and generate a physical map of genomes, genes, or other segments of DNA.
Short sequences (generally about 10 base pairs) of DNA that are complementary to sequences of messenger RNA and allow reverse transcriptases to start copying the adjacent sequences of mRNA. Primers are used extensively in genetic and molecular biology techniques.
Any method used for determining the location of and relative distances between genes on a chromosome.
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.
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.
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.
Variant forms of the same gene, occupying the same locus on homologous CHROMOSOMES, and governing the variants in production of the same gene product.
A mutation in which a codon is mutated to one directing the incorporation of a different amino acid. This substitution may result in an inactive or unstable product. (From A Dictionary of Genetics, King & Stansfield, 5th ed)
A method (first developed by E.M. Southern) for detection of DNA that has been electrophoretically separated and immobilized by blotting on nitrocellulose or other type of paper or nylon membrane followed by hybridization with labeled NUCLEIC ACID PROBES.
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.
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.
A variation of the PCR technique in which cDNA is made from RNA via reverse transcription. The resultant cDNA is then amplified using standard PCR protocols.
The degree of similarity between sequences of amino acids. This information is useful for the analyzing genetic relatedness of proteins and species.
A form of GENE LIBRARY containing the complete DNA sequences present in the genome of a given organism. It contrasts with a cDNA library which contains only sequences utilized in protein coding (lacking introns).
A genetic rearrangement through loss of segments of DNA or RNA, bringing sequences which are normally separated into close proximity. This deletion may be detected using cytogenetic techniques and can also be inferred from the phenotype, indicating a deletion at one specific locus.
Any of the processes by which nuclear, cytoplasmic, or intercellular factors influence the differential control (induction or repression) of gene action at the level of transcription or translation.
The outward appearance of the individual. It is the product of interactions between genes, and between the GENOTYPE and the environment.
Works containing information articles on subjects in every field of knowledge, usually arranged in alphabetical order, or a similar work limited to a special field or subject. (From The ALA Glossary of Library and Information Science, 1983)
A benign familial disorder, transmitted as an autosomal dominant trait. It is characterized by low-grade chronic hyperbilirubinemia with considerable daily fluctuations of the bilirubin level.
The pattern of GENE EXPRESSION at the level of genetic transcription in a specific organism or under specific circumstances in specific cells.
That part of the genome that corresponds to the complete complement of EXONS of an organism or cell.
Production of new arrangements of DNA by various mechanisms such as assortment and segregation, CROSSING OVER; GENE CONVERSION; GENETIC TRANSFORMATION; GENETIC CONJUGATION; GENETIC TRANSDUCTION; or mixed infection of viruses.
A set of three nucleotides in a protein coding sequence that specifies individual amino acids or a termination signal (CODON, TERMINATOR). Most codons are universal, but some organisms do not produce the transfer RNAs (RNA, TRANSFER) complementary to all codons. These codons are referred to as unassigned codons (CODONS, NONSENSE).
Large aggregates of CELESTIAL STARS; COSMIC DUST; and gas. (From McGraw Hill Dictionary of Scientific and Technical Terms, 6th ed)
The science concerned with celestial bodies and the observation and interpretation of the radiation received in the vicinity of the earth from the component parts of the universe (McGraw Hill Dictionary of Scientific and Technical Terms, 5th ed)
Aggregates of matter in outer space, such as stars, planets, comets, etc. and the properties and processes they undergo.
The determination of the pattern of genes expressed at the level of GENETIC TRANSCRIPTION, under specific circumstances or in a specific cell.
Hybridization of a nucleic acid sample to a very large set of OLIGONUCLEOTIDE PROBES, which have been attached individually in columns and rows to a solid support, to determine a BASE SEQUENCE, or to detect variations in a gene sequence, GENE EXPRESSION, or for GENE MAPPING.

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)

To test the quality of the new algorithm, several well-known genes with clusters of mutually exclusive exons with different characteristics were analysed (Figure 3). The first test case is the cytoplasmic dynein heavy chain from Schistosoma mansoni (Sm DHC1). Dynein heavy chains belong to the longest genes in eukaryotes encoding 4000 - 5000 residues and are spread over several dozens of exons. The mutually exclusive exon is clearly identified in the middle of the gene, encoding split codons at the 3- and 5-end of the exon. The query exon and the candidate exon have identical lengths and show strong homology. Based on the multiple sequence alignment of more than 2000 DHCs these exons are mutually exclusive and not constitutive or differentially included. The second case represents the muscle myosin heavy chain gene from the waterflea Daphnia magna[19]. The arthropod muscle myosin heavy chain genes contain several clusters of mutually exclusive exons to fine tune the mechanochemical ...
Alternative exon usage (AEU) is an important component of gene regulation. Exon expression platforms allow the detection of associations between AEU and phenotypes such as cancer. Numerous studies have identified associations between gene expression and the brain cancer glioblastoma multiforme (GBM). The few consistent gene expression biomarkers of GBM that have been reported may be due to the limited consideration of AEU and the analytical approaches used. The objectives of this study were to develop a model that accounts for the variations in expression present between the exons within a gene and to identify AEU biomarkers of GBM survival. The expression of exons corresponding to 25,403 genes was related to the survival of 250 individuals diagnosed with GBM in a training data set. Genes exhibiting AEU in the training data set were confirmed in an independent validation data set of 78 patients. A hierarchical mixed model that allows the consideration of covariation between exons within a gene and of
This track shows the genomic locations of the probesets and probes from the Affymetrix Exon array. This array was designed to interrogate every known and putative exon in the human genome. For the design of this array, Affymetrix compiled evidence of expression from sources including well-annotated genes such as RefSeq, genomic alignments of mRNA and EST sequences, gene predictions, exon predictions, and regions that are syntenic to conserved regions in related species. Using this evidence, Affymetrix designed a probeset for each known or putative exon. While some of these regions might never be transcribed, the goal is to obtain a comprehensive measurement of transcription in the human genome. In most cases, this array contains one probeset per exon. However, whenever this design-time evidence suggested that some exon had alternative splice sites, the exon was subdivided into two or more regions, and one probeset was designed for each region (where possible). The array contains no probesets for ...
This study addresses two important aspects of TMPRSS2-ERG expression in prostate cancer. First of all, a remarkable difference in expression characteristics was detected between TMPRSS2(exon 1) and TMPRSS2(exon 1)-ERG transcripts on the one hand and TMPRSS2(exon 0) and TMPRSS2(exon 0)-ERG transcripts on the other hand. Secondly, the clinical data indicated a more favorable prognosis for prostate cancer patients expressing TMPRSS2(exon 0)-ERG transcripts.. It is estimated that almost half of all genes in the human genome contain more than one first exon as an important mechanism to regulate gene expression (19). Here, we showed that TMPRSS2 transcripts starting at exon 0 were much more prostate specific than those starting at exon 1 (Fig. 1B) and that the expression level of transcripts containing exon 0 was much more variable (Fig. 1D). TMPRSS2 exon 0 is located in a retroviral repeat element, ERVL-B4 (Fig. 1A). This repeat does not contain a standard long terminal repeat promoter element; ...
An additional nicety would be to somehow work in a preference for 5 exons. For example, lets say a gene has 3 exons and, with the expression data, all 3 exons are equally expressed. Id like to selectively get the first 2 exons. Ive started learning Galaxy and was able to import BED files for UCSC exons (as in the Galaxy 101 tutorial) and a BED file for Affy microarray expression data. (I tried also importing the Burge RNA-seq track as BED but couldnt get it to work). I did an inner join on genomic sequences to join the expression data with the exons and sorted them from most expressed to least. But how do I sort within genes? That is, how do I get the top 2 exons per gene (highest expressing exons per gene) and, if there are more than 2 with equally high expression, how do I preferentially get the 5` exons? Im also open to ways to do this without using Galaxy, etc. I want to do this for an entire genome, so I figured it would be good to have a Galaxy workflow, which I could then apply to ...
Exon shuffling was first introduced in 1978 when Walter Gilbert discovered that the existence of introns could play a major role in the evolution of proteins. It was noted that recombination within introns could help assort exons independently and that repetitive segments in the middle of introns could create hotspots for recombination to shuffle the exonic sequences. However, the presence of these introns in eukaryotes and absence in prokaryotes created a debate about the time in which these introns appeared. Two theories arose: the introns early theory and the introns late theory. Supporters of the introns early theory believed that introns and RNA splicing were the relics of the RNA world and therefore both prokaryotes and eukaryotes had introns in the beginning. However, prokaryotes eliminated their introns in order to obtain a higher efficiency, while eukaryotes retained the introns and the genetic plasticity of the ancestors. On the other hand, supporters of the introns late theory ...
DNA microarrays and RNAseq are complementary methods for studying RNA molecules. Current computational methods to determine alternative exon usage (AEU) using such data require impractical visual inspection and still yield high false-positive rates. Integrated Gene and Exon Model of Splicing (iGEMS) adapts a gene-level residuals model with a gene size adjusted false discovery rate and exon-level analysis to circumvent these limitations. iGEMS was applied to two new DNA microarray datasets, including the high coverage Human Transcriptome Arrays 2.0 and performance was validated using RT-qPCR. First, AEU was studied in adipocytes treated with (n = 9) or without (n = 8) the anti-diabetes drug, rosiglitazone. iGEMS identified 555 genes with AEU, and robust verification by RT-qPCR (∼90%). Second, in a three-way human tissue comparison (muscle, adipose and blood, n = 41) iGEMS identified 4421 genes with at least one AEU event, with excellent RT-qPCR verification (95%, n = 22). Importantly, iGEMS ...
TY - JOUR. T1 - Tissue-specific splicing regulator Fox-1 induces exon skipping by interfering E complex formation on the downstream intron of human F1γ gene. AU - Fukumura, Kazuhiro. AU - Kato, Ayako. AU - Jin, Yui. AU - Ideue, Takashi. AU - Hirose, Tetsuro. AU - Kataoka, Naoyuki. AU - Fujiwara, Toshinobu. AU - Sakamoto, Hiroshi. AU - Inoue, Kunio. PY - 2007/8/1. Y1 - 2007/8/1. N2 - Fox-1 is a regulator of tissue-specific splicing, via binding to the element (U)GCAUG in mRNA precursors, in muscles and neuronal cells. Fox-1 can regulate splicing positively or negatively, most likely depending on where it binds relative to the regulated exon. In cases where the (U)GCAUG element lies in an intron upstream of the alternative exon, Fox-1 protein functions as a splicing repressor to induce exon skipping. Here we report the mechanism of exon skipping regulated by Fox-1, using the hF1γ gene as a model system. We found that Fox-1 induces exon 9 skipping by repressing splicing of the downstream intron 9 ...
Due to the inclusive nature of our genome-wide exon microarrays, we are able to discover novel alternative splicing patterns in addition to monitoring known splicing events. As technology allows for smaller feature sizes, it will be possible to include larger numbers of probes per array, thereby increasing the feasibility of large-scale non-biased designs. Microarray designs that are more inclusive and less dependent on current genome annotations will ultimately aid in the development of tools that are designed to annotate, rather than the other way around. For example, recent work using a similar design concept based on the mouse genome was able to refine gene boundaries using co-regulation of exons across many different tissue types [43]. However, our data suggest that there is a large amount of expression outside of well annotated exons. Reliance on any one single exon prediction algorithm or sequence content source will likely result in incomplete coverage.. Exon microarrays represent a huge ...
Genemark = Bio::Tools::Genemark-,new(-file =, result.Genemark); # filehandle: $Genemark = Bio::Tools::Genemark-,new( -fh =, \*INPUT ); # parse the results # note: this class is-a Bio::Tools::AnalysisResult which implements # Bio::SeqAnalysisParserI, i.e., $Genemark-,next_feature() is the same while($gene = $Genemark-,next_prediction()) { # $gene is an instance of Bio::Tools::Prediction::Gene, which inherits # off Bio::SeqFeature::Gene::Transcript. # # $gene-,exons() returns an array of # Bio::Tools::Prediction::Exon objects # all exons: @exon_arr = $gene-,exons(); # initial exons only @init_exons = $gene-,exons(Initial); # internal exons only @intrl_exons = $gene-,exons(Internal); # terminal exons only @term_exons = $gene-,exons(Terminal); # singleton exons: ($single_exon) = $gene-,exons(); } # essential if you gave a filename at initialization (otherwise the file # will stay open) $Genemark-,close ...
Dopamine D4 receptor exon III genotype influence on the auditory evoked novelty P3.: The functional implications of the dopamine D4 receptor gene (DRD4) exon II
Comparative analysis of exon/intron organization of genes and their resulting protein structures is important for understanding evolutionary relationships between species, rules of protein organization, and protein functionality. We present SEDB, the Structural Exon Database, with a web interface, an application which allows users to retrieve the exon/intron organization of genes and map the location of the exon boundaries and intron phase onto a multiple structural alignment. SEDB is linked with Friend, an integrated analytical multiple sequence/structure viewer, which allows simultaneous visualization of exon boundaries on structure and sequence alignments. With SEDB researchers can study the correlations of gene structure with the properties of the encoded three-dimensional protein structures across eukaryotic organisms ...
The properties of genotype-phenotype landscapes are crucial for understanding evolution but are not characterized for most traits. Here, we present a ,95% complete local landscape for a defined molecular function-the alternative splicing of a human exon (FAS/CD95 exon 6, involved in the control of apoptosis). The landscape provides important mechanistic insights, revealing that regulatory information is dispersed throughout nearly every nucleotide in an exon, that the exon is more robust to the effects of mutations than its immediate neighbours in genotype space, and that high mutation sensitivity (evolvability) will drive the rapid divergence of alternative splicing between species unless it is constrained by selection. Moreover, the extensive epistasis in the landscape predicts that exonic regulatory sequences may diverge between species even when exon inclusion levels are functionally important and conserved by selection ...
Protein tyrosine phosphatase CD45 is a key player in T-cell receptor signaling and lymphocyte development. Differential expression of multiple CD45 isoforms resulting from the alternative splicing of exons A, B, and C, which encode part of the extracellular domain, is an important feature of CD45 expression. We report a novel isoform that results from the alternative splicing of a previously undiscovered exon between the constitutively spliced exon 3 and the alternatively spliced exon A. This 123-bpâ€:#x0093:long exon encodes 41 amino acids and is unlikely to undergo te extensive glycosylation seen for the regions encoded by exons A, B, and C. Reverse transcriptase polymerase chain reaction demonstrates that this isoform is expressed in human peripheral blood mononuclear cells and cell lines of lymphoid origin, but with a clearly different pattern to that of the isoforms caused by exons A, B, and C, implying a different regulatory mechanism.
The recently released Exon arrays differ from the previous 3 arrays in terms of the number, placement and annotational confidence of oligonucleotide probes. As a result, new methods that take advantage of Exon array design features can improve gene-level expression estimates. In this manuscript we propose a strategy for computing gene expression indices on Exon arrays that combines a probe-specific background correction with a probe selection procedure. Analysis of independent SAGE data demonstrates that A/P calls generated from the MAT background model offer substantial improvements. This improvement is likely due to both the increased number of probes per gene and the improvement of the MAT background model over the default Affymetrix background correction. Furthermore, we observed that Exon array gene expression indices show a high degree of correlation between human and mouse orthologs.. This work represents a step in the continued development of accurate gene-level expression estimates ...
Although unicellular eukaryotes such as yeast have either no introns or very few, metazoans and especially vertebrate genomes have a large fraction of non-coding DNA. 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.[5] This can provide a practical advantage in omics-aided health care (such as precision medicine) because it makes commercialized whole exome sequencing a smaller and less expensive challenge than commercialized whole genome sequencing. The large variation in genome size and C-value across life forms has posed an interesting challenge called the C-value enigma. Across all eukaryotic genes in GenBank there were (in 2002), on average, 5.48 exons per gene. The average exon encoded 30-36 amino acids.[6] While the longest exon in the human genome is 11555 bp long, several exons have been found to be only 2 bp long.[7] A single-nucleotide exon has been reported from the Arabidopsis ...
patients (13% of all patients), while exon 45 and 53 skipping would both individually be applicable to 8% of the patients (Aartsma-Rus et al. 2009a). AONs to skip each individual exon have been identified and theoretically exon skipping would be applicable to 80% of deletions, 91% of small mutations and 73% of duplications, or 83% of all patients (Table 5.2).. However, mutations in the essential cysteine-rich domain invariably cause DMD, regardless of whether deletions are in-frame or out-of-frame (Aartsma-Rus et al. 2006b). Thus, for patients with mutations in the part of the transcripts that encodes the cysteine-rich domain (exons 64-70, Fig. 5.1) exon skipping will in all likelihood not be beneficial. Since there are two N-terminal actin-binding domains, and a third domain located in the central rod domain (Fig. 5.1), there is more flexibility for deletions affecting one or two actin-binding domains, as the additional domains retain some of the functionality (Aartsma-Rus et al. 2006b). ...
Detection of exon junctions in single cells within the tissue environment is possible by using only one ZZ probe uniquely designed on the specific exon junction of interest. For an example of the detection of a sequence with specific exon skipping, METΔ14 (Frampton GM et al, Cancer Discovery, 2015; Awad MM et al, J Clin Oncol, 2016) where 3 probes are designed (image 1): one control probe designed for an exon junction present in all MET transcripts (exon junction 12/13), one probe designed for the exon junction with exon 14 (exon junction 14/15), and one probe designed for the exon junction with exon 14 skipping (exon junction 13/15). Figure 2 shows an example of the BaseScope™ assay used for the detection of METΔ14 in cell lines ...
Tumor-predominant splice isoforms were identified during comparative in silico sequence analysis of EST clones, suggesting that global aberrant alternative pre-mRNA splicing may be an epigenetic phenomenon in cancer. We used an exon expression array to perform an objective, genome-wide survey of glioma-specific splicing in 24 GBM and 12 nontumor brain samples. Validation studies were performed using RT-PCR on glioma cell lines, patient tumor and nontumor brain samples. In total, we confirmed 14 genes with glioma-specific splicing; seven were novel events identified by the exon expression array (A2BP1, BCAS1, CACNA1G, CLTA, KCNC2, SNCB, and TPD52L2). Our data indicate that large changes (| 5-fold) in alternative splicing are infrequent in gliomagenesis (| 3% of interrogated RefSeq entries). The lack of splicing changes may derive from the small number of splicing factors observed to be aberrantly expressed. While we observed some tumor-specific alternative splicing, the number of genes showing exclusive
Abstract: Cultured muscle cells from DMD patients carrying duplications were transfected with AONs targeting the duplicated exons, and the dystrophin RNA and protein were analyzed.For two brothers with an exon 44 duplication, skipping was, even at suboptimal transfection conditions, so efficient that both exons 44 were skipped, thus generating, once more, an out-of-frame transcript. In such cases, one may resort to multi-exon skipping to restore the reading frame, as is shown here by inducing skipping of exon 43 and both exons 44. By contrast, in cells from a patient with an exon 45 duplication we were able to induce single exon 45 skipping, which allowed restoration of wild type dystrophin. The correction of a larger duplication (involving exons 52 to 62), by combinations of AONs targeting the outer exons, appeared problematic due to inefficient skipping and mistargeting of original instead of duplicated exons.The correction of DMD duplications by exon skipping depends on the specific exons ...
An exon is any part of a gene that will encode a part of the final mature RNA produced by that gene after introns have been removed by RNA splicing. The term exon refers to both the DNA sequence within a gene and to the corresponding sequence in RNA transcripts. In RNA splicing, introns are removed and exons are covalently joined to one another as part of generating the mature messenger RNA. Just as the entire set of genes for a species constitutes the genome, the entire set of exons constitutes the exome. 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. This definition was originally made for protein-coding transcripts that are spliced before being translated. The term later ...
The Fgf2 gene is expressed in the brain neuroepithelium during embryonic development and in astroglial cells throughout life. Previous knockout studies suggested that FGF2 plays a role in the proliferation of neural progenitors in the embryonic cerebral cortex. These studies exclusively used knockout alleles lacking the Fgf2 exon 1. However, the description of putative alternative exons located downstream from the canonical exon 1 raised the possibility that alternatively spliced transcripts may compensate for the lack of the canonical exon 1 in the Fgf2 -/- mice. We generated and characterized a new line of Fgf2 knockout mice lacking the expression of exon 3, which is conserved in all Fgf2 transcripts and contains essential heparin and receptor binding interfaces. The expression of Fgf2 exon 3 was prevented by inserting a transcriptional STOP cassette in the Fgf2 genomic locus. These mice demonstrate a phenotype in the adult neocortex characterized by decreased density and number of cortical excitatory
mzef = Bio::Tools::MZEF-,new(-file =, result.mzef); # filehandle: $mzef = Bio::Tools::MZEF-,new( -fh =, \*INPUT ); # to indicate that the sequence was reversed prior to feeding it to MZEF # and that you want to have this reflected in the strand() attribute of # the exons, as well have the coordinates translated to the non-reversed # sequence $mzef = Bio::Tools::MZEF-,new( -file =, result.mzef, -strand =, -1 ); # parse the results # note: this class is-a Bio::Tools::AnalysisResult which implements # Bio::SeqAnalysisParserI, i.e., $genscan-,next_feature() is the same while($gene = $mzef-,next_prediction()) { # $gene is an instance of Bio::Tools::Prediction::Gene # $gene-,exons() returns an array of # Bio::Tools::Prediction::Exon objects # all exons: @exon_arr = $gene-,exons(); # internal exons only @intrl_exons = $gene-,exons(Internal); # note that presently MZEF predicts only internal exons! } # essential if you gave a filename at initialization (otherwise the file # will stay open) ...
In human pre-mRNA splicing, infrequent errors occur resulting in erroneous splice products as shown in a genome-wide approach. One characteristic subgroup consists of products lacking one cassette exon. The noise in the splicing process, represented by those misspliced products, can be increased by cold shock treatment or by inhibiting the nonsense mediated decay. Here, we investigated whether the splicing noise frequency increases with age in vivo in peripheral bloods cells or in vitro in cultured and aged fibroblasts from healthy donors. Splicing noise frequency was measured for four erroneously skipped NF1 exons and one exon of RABAC1, AATF and PCGF2 by RT-qPCR. Measurements were validated in cultured fibroblasts treated with cold shock or puromycin. Intragenic but not interpersonal differences were detected in splicing noise frequencies in vivo in peripheral blood cells of 11 healthy donors (15 y-85 y) and in in vitro senescent fibroblasts from three further donors. No correlation to the age of the
While, characterizing the hAT1R gene it was demonstrated that ≥4 alternatively spliced hAT1R mRNAs were transcribed in human tissues (Figure 1).33,34 The hAT1R mRNA splice variants were composed of the following exons: exons 1 and 4; exons 1, 2, and 4; exons 1, 3, and 4; and exons 1, 2, 3, and 4; therefore, alternatively spliced hAT1R mRNAs differ only in the inclusion or exclusion of exon 2 and/or 3 (reviewed in Reference 37).. Splice variants that harbor exon 2 are functionally interesting because they contain 2 upstream AUG start codons (Figure 1),34,38 which are predicted to generate upstream ORFs (uORFs) of different lengths. PCR analysis demonstrated that hAT1R mRNA splice variants, which included exon 2 (ie, exons 1, 2, and 4), were composed of ≥30% of the total hAT1R mRNA transcripts expressed in a given tissue; this suggests that this splice variant is physiologically important.34,38-40 Curnow et al34 and Warnecke et al38 demonstrated that the presence of exon 2 inhibited the ...
The genetic change was a single base (G) insertion in exon 25 of the cardiac MyBP-C gene on chromosome 11, which resulted in a sequence suitable to serve as a 5′ splice donor site (AG GTGGG). This mutation was also recently reported in a nonrelated family of the same ethnic group in North America.10 We showed that the mutation resulted in the loss of 40 bp at the 3′ end of exon 25 in mRNA extracted from affected myocardial tissue. This loss resulted in a premature translational stop, which was then predicted to result in a truncated protein of 95 kDa and the loss of the C-terminal binding sites for myosin heavy chain and titin.20 A reading shift would also occur if mRNA splicing were unaffected by the inserted G in exon 25. In this case, the shift resulting from the additional G would lead to a premature stop 40 residues away from the 3′ terminal of codon 792. However, such mutated mRNA was not observed (data not shown).. The shortened 95-kDa MyBP-C protein was not detected in ...
Abstract Background To date, exon capture has largely been restricted to species with fully sequenced genomes, which has precluded its applicat
DNA is made up of different units called nucleotides. There are a variety of four different nucleotides that make up the polymer that is DNA[1]. DNA consists of two different regions, one being exons and the other introns. The regions of exons in the DNA consist of fewer nucleotides than the regions of introns and are the regions that code for proteins[2]. It is also now thought that enhancer sequences for regulation of gene transcription is not just found in introns but also exons.[3]. Exons are the coding regions of a gene and are separated by regions of introns; they are copied during transcription (along with introns) to produce pre-mRNA[4] ...
OBJECTIVE: To investigate the expression of the familial Mediterraneanfever (FMF) gene (MEFV) in human synovial fibroblasts. METHODS: MEFVmessenger RNA in synovial fibroblasts, chondrocytes, and peripheral bloodleukocytes (PBLs) was analyzed by semiquantitative and real-timepolymerase chain reaction and ribonuclease protection assay. Thesubcellular localization of pyrin, the MEFV product, was determined intransfected synovial fibroblasts and HeLa cells with plasmids encodingpyrin isoforms. Native pyrin was detected with an antipyrin antibody.RESULTS: MEFV was expressed in synovial fibroblasts, but not inchondrocytes. Four alternatively spliced transcripts were identified: anextension of exon 8 (exon 8ext) resulting in a frameshift that predicts atruncated protein lacking exons 9 and 10, the addition of an exon (exon4a) predicting a truncated protein at exon 5, the in-frame substitution ofexon 2a for exon 2, and the previously described removal of exon 2 (exon2Delta). Exon 8ext transcripts ...
The classification of human gene sequences into exons and introns is a difficult problem in DNA sequence analysis. In this paper, we define a set of features, called the simple Z (SZ) features, which is derived from the Z-curve features for the recognition of human exons and introns. The classification results show that SZ features, while fewer in numbers ~three in total!, can preserve the high recognition rate of the original nine Z-curve features. Since the size of SZ features is one-third of the Z-curve features, the dimensionality of the feature space is much smaller, and better recognition efficiency is achieved. If the stop codon feature is used together with the three SZ features, a recognition rate of up to 92% for short sequences of length ,140 bp can be obtained ...
The complete exon size and distribution pattern in the gene for the alpha 1 chain of human type IV collagen was determined. Clones covering 145 kilobases (kb) of genomic DNA including 100 kb of the gene itself as well as 25 kb upstream and 20 kb downstream of the gene sequences, respectively, were isolated from lambda phage and cosmid libraries. The overall gene structure was determined by endonuclease restriction mapping and R-loop analyses and all exon sizes by nucleotide sequencing. The characterized clones contained all the coding sequences except for exon 2 whose sequence was determined after its amplification by the polymerase chain reaction. There were four gaps in the intron sequences; the exact size of the gene is unknown. The entire gene is at least 100 kb in size and contains 52 exons whose size distribution is completely different from that of the genes for fibrillar collagens. In the -Gly-X-Y- coding region there are three exons of 99, 90, and 45 base pairs (bp) each and two exons ...
Hi everyone, I need a bed file containing starts and ends of the exons, gene name and number of the exon - but just for the canonical transcript - because I dont want to have the regions repeated. I tried UCSC Table browser and BioMart but non of them gives me exactly what I need.. Using UCSC I can get canonical transcripts (but at the same time I couldnt get starts and ends of the exon altogether with the gene name).. Using BioMart I can get starts and ends of the exons altogether with the gene name, but I cant find how to choose the canonical transcripts and thats why the regions are repeated as seen below in the case of NUS1P3:. ...
Digital processing of a nucleotide sequence requires it to be mapped to a numerical sequence in which the choice of nucleotide to numeric mapping affects how well its biological properties can be preserved and reflected from nucleotide domain to numerical domain. Digital spectral analysis of nucleotide sequences unfolds a period-3 power spectral value which is more prominent in an exon sequence as compared to that of an intron sequence. The success of a period-3 based exon and intron classification depends on the choice of a threshold value. The main purposes of this article are to introduce novel codes for 1-sequence numerical representations for spectral analysis and compare them to existing codes to determine appropriate representation, and to introduce novel thresholding methods for more accurate period-3 based exon and intron classification of an unknown sequence. The main findings of this study are summarized as follows: Among sixteen 1-sequence numerical representations, the K-Quaternary Code I
Digital processing of a nucleotide sequence requires it to be mapped to a numerical sequence in which the choice of nucleotide to numeric mapping affects how well its biological properties can be preserved and reflected from nucleotide domain to numerical domain. Digital spectral analysis of nucleotide sequences unfolds a period-3 power spectral value which is more prominent in an exon sequence as compared to that of an intron sequence. The success of a period-3 based exon and intron classification depends on the choice of a threshold value. The main purposes of this article are to introduce novel codes for 1-sequence numerical representations for spectral analysis and compare them to existing codes to determine appropriate representation, and to introduce novel thresholding methods for more accurate period-3 based exon and intron classification of an unknown sequence. The main findings of this study are summarized as follows: Among sixteen 1-sequence numerical representations, the K-Quaternary Code I
In this work, organization, expression and function of the human Peroxisomal Testis-specific 1 (PXT1) gene were investigated. The mRNA of the human PXT1 gene doesnt contain two exons as known so far, but five exons. The expression of three putative upstream exons was confirmed in this work. The results of the qualitative and quantitative real-time PCR show that the exon 1 consists of three variously spliced units (exons 1a, 1b and 1c). The human PXT1 gene is subjected to alternative splicing, of which exons 1b, 1c, 2 and 4 are concerned, which was shown by sequence analysis. In total, six transcripts were identified. The additional exons have an impact on the protein structure due to the extension of the ORF coding for 51 amino acids previously to 134 now. In the longer protein the BH3 interacting domain (BID) is detected which has a known proapoptotic function. Due to the alternatively spliced exon 4 and the resulting frameshift a truncated protein exists and in its mRNA a premature stop codon ...
Nous montrons lutilisation de la puce exon dAffymetrix pour lanalyse simultanée de lexpression des gènes et de la variation disoformes. Nous avons utilisé les échantillons dARN du cerveau et des tissus de référence qui ont été antérieurement utilisés dans létude du consortium MicroArray Quality Control (MAQC). Nous démontrons une forte concordance de la quantification de lexpression des gènes entre trois plateformes dexpression populaires à savoir la puce exon dAffymetrix, la puce Illumina et la puce U133A dAffymetrix. Plus intéressant nous montrons que la majorité des discordances entre les trois plateformes résulterait des positions différentes des sondes à travers les plateformes et que les variations disoforme exactes ne peuvent être identifiées que par la puce exon. Nous avons détecté avec succès, entre les tissus de référence et ceux du cerveau, une centaine de cas dévènements dépissage alternatif. La puce exon est requise dans lanalyse de ...
Aims to balance the goal of giving the complete picture of possible coding exons, with the need to stay grounded in terms of the verifiability of the actual function of the sequences it collects. Thus it relies on the ENSEMBLs annotation of known (known here being the actual annotation term used, hence the quotes) human exons as the anchor for the search and for the results presentation. To these, ExoLocator adds the search for ostensibly missing exons in orthologous protein pairs across species, using an extensive computational pipeline to narrow down the search region for the candidate exons and find a suitable template in the other species, as well as state-of-the-art implementations of pairwise alignment algorithms. The resulting complements of exons are organized in a way currently unique to ExoLocator: multiple sequence alignments, both on the nucleotide and on the peptide levels, clearly indicating the exon boundaries. The alignments can be inspected in the web-embedded viewer, downloaded or
Author Summary Changes in gene regulation have long been known to play important roles in both innate and adaptive immune responses. While transcriptional responses to infection have been well-characterized, much less is known about the extent to which co-transcriptional mechanisms of mRNA processing are involved in the regulation of immune defenses. In this study, we sought to investigate the role of mRNA processing in the cellular responses of human macrophages to live bacterial infection. Using primary human macrophages derived from whole blood samples from 60 individuals, we sequenced mRNA both before and after infection with two live bacteria. We show that immune responses to infection are accompanied by pervasive changes in mRNA isoform usage, with systematic shifts towards increased cassette exon inclusion and shortening of Tandem 3 UTRs post-infection. These patterns are conserved in nonhuman primates, supporting their functional importance across evolutionary time. Complementary microRNA
Author Summary Changes in gene regulation have long been known to play important roles in both innate and adaptive immune responses. While transcriptional responses to infection have been well-characterized, much less is known about the extent to which co-transcriptional mechanisms of mRNA processing are involved in the regulation of immune defenses. In this study, we sought to investigate the role of mRNA processing in the cellular responses of human macrophages to live bacterial infection. Using primary human macrophages derived from whole blood samples from 60 individuals, we sequenced mRNA both before and after infection with two live bacteria. We show that immune responses to infection are accompanied by pervasive changes in mRNA isoform usage, with systematic shifts towards increased cassette exon inclusion and shortening of Tandem 3 UTRs post-infection. These patterns are conserved in nonhuman primates, supporting their functional importance across evolutionary time. Complementary microRNA
Does anyone have any information on these exons. I know exon skipping is not an option because of the complexity of these exons but that is where my knowledge…
Like CB1R, the CB2R coding region is contained in a single exon and is flanked by upstream noncoding exons in human, mouse, and, debatably, rat. Human CB2R consists of three exons alternatively transcribed and spliced to yield isoforms CB2A and -B (Liu et al., 2009). CB2B, the first cloned cDNA, is transcribed from a promoter proximal to exon2 and expressed most highly in immune cells and tissues. The more recently identified CB2A contains exon1 and exon3 and is generated from a promoter 5′ proximal to exon1. In contrast to CB2B, CB2A is most highly expressed in testis and shows some expression in the brain.. Mouse CB2R similarly consists of three exons alternatively transcribed by two promoters (Onaivi et al., 2006; Liu et al., 2009). In contrast to humans, however, both CB2A and CB2B are expressed predominantly in the spleen (Liu et al., 2009). Rat CB2R gene structure seems more complex than that of human and mouse, although findings are conflicting. In Fig. 1, we present findings by Liu et ...
1. In the context of a new mammalian model organism recently sequenced and annotated, gene YFG has 3 introns and 4 exons. Databases show that there are 3 different lengths of cDNA sequences associated with Gene YFG. One of these cDNA sequences has three out of four exons plus additional nucleotide sequence at the 3 end of the cDNA. This part codes for an extra 123 amino acids. Annotated gene UB2, appears immediately downstream of YFG. UB2 has a single exon coding for 123 amino acids matching the cDNA. There is no cDNA in your database encoding for a UB2 gene with these 123 amino acids at the N-terminus ...
antibody-antibodies.com is the marketplace for research antibodies. Find the right antibody for your research needs. The identification of a new alternative exon with highly restricted tissue expression in transcripts encoding the mouse Pgp-1 (CD44) homing receptor. Comparison of all 10 variable exons between mouse, human, and rat.
RNA modification must be performed in order to form the various proteins needed for eukaryotes to function. RNA modification generates mature RNA. Through RNA modification, a eukaryotic cell can use fewer variations in base pairs of the genetic code (DNA and RNA) while creating proteins with diverse functions. One of the most common methods employed by eukaryotes is to use spliceosomes to cleave out introns (intervening sequences/ non coding proteins) of the pre-RNA, leaving only exons (expressed sequences/coding proteins). Cutting out the intron segments allows for the possibility of exon to rearrangement. Spicing all exons together is called mature mRNA.. Whats the advantage of spitting genes? Exons are segments that coding proteins and give proteins specific functions. This leads to the concept of exon shuffling. Exons shuffling is the rearrangement of the exons in the mRNA. These mRNA will come up with different types of proteins with different functions, binding sites, and catalytic sites. ...
Supplement Genes contain exons which are regions coding for proteins and which are interrupted by the unused sequences called introns. Exons have been found to include both sequences coding for amino acids and untranslated sequences. The introns are removed and the exons are joined together to form the final functional mRNA. ...
This sequence change affects codon 6 of the SLC2A1 mRNA. It is a silent change, meaning that it does not change the encoded amino acid sequence of the SLC2A1 protein. This variant also falls at the last nucleotide of exon 1 of the SLC2A1 coding sequence, which is part of the consensus splice site for this exon. The frequency data for this variant in the population databases is considered unreliable, as metrics indicate insufficient coverage at this position in the ExAC database. This variant has not been reported in the literature in individuals with SLC2A1-related conditions. ClinVar contains an entry for this variant (Variation ID: 378602). Nucleotide substitutions within the consensus splice site are a relatively common cause of aberrant splicing (PMID: 17576681, 9536098). Algorithms developed to predict the effect of sequence changes on RNA splicing suggest that this variant may disrupt the consensus splice site, but this prediction has not been confirmed by published transcriptional ...
The gene spans approximately 23 kilobases and is composed of 21 exons interrupted by 20 introns. Exon sizes range from 52 bases (exon 7) to over 1200 bases (exon 21), intron sizes from 68 bases (intron L) to 10.8 kilobases (intron A). The splice sites for donor and acceptor were in agreement with the canonical GT/AG rule. Functional regions of beta ARK are described with respect to their location within the exon-intron organization of the gene. Primer extension and RNase protection assays suggest a major transcription start site approximately 246 bases upstream of the start ATG. Sequence analysis of the 5-flanking/promoter region reveals many features characteristic of mammalian housekeeping genes, i.e. the lack of a TATA box, an absent or nonstandard positioned CAAT box, high GC content, and the presence of Sp1-binding sites. The extraordinarily high GC content of the 5-flanking region (, 80%) helps define this region as a CpG island that may be a principal regulator of beta ARK ...
RefSeq Summary (NM_002116): HLA-A belongs to the HLA class I heavy chain paralogues. This class I molecule is a heterodimer consisting of a heavy chain and a light chain (beta-2 microglobulin). The heavy chain is anchored in the membrane. Class I molecules play a central role in the immune system by presenting peptides derived from the endoplasmic reticulum lumen. They are expressed in nearly all cells. The heavy chain is approximately 45 kDa and its gene contains 8 exons. Exon 1 encodes the leader peptide, exons 2 and 3 encode the alpha1 and alpha2 domains, which both bind the peptide, exon 4 encodes the alpha3 domain, exon 5 encodes the transmembrane region, and exons 6 and 7 encode the cytoplasmic tail. Polymorphisms within exon 2 and exon 3 are responsible for the peptide binding specificity of each class one molecule. Typing for these polymorphisms is routinely done for bone marrow and kidney transplantation. Hundreds of HLA-A alleles have been described. [provided by RefSeq, Jul 2008 ...
Approximately two-thirds of Duchenne muscular dystrophy (DMD) patients show intragenic deletions ranging from one to several exons of the DMD gene and leading to a premature stop codon. Other deletions that maintain the translational reading frame of the gene result in the milder Becker muscular dystrophy (BMD) form of the disease. Thus the opportunity to transform a DMD phenotype into a BMD phenotype appeared as a new treatment strategy with the development of antisense oligonucleotides technology, which is able to induce an exon skipping at the pre-mRNA level in order to restore an open reading frame. Because the DMD gene contains 79 exons, thousands of potential transcripts could be produced by exon skipping and should be investigated. The conventional approach considers skipping of a single exon. Here we report the comparison of single- and multiple-exon skipping strategies based on bioinformatic analysis. By using the Universal Mutation Database (UMD)-DMD, we predict that an optimal multiexon
Several cross-sectional studies have demonstrated the relevance of DNA methylation of the glucocorticoid receptor exon 1F region (GR-1F) for trauma-related psychopathology. We conducted a longitudinal study to examine GR-1F methylation changes over time in relation to trauma exposure and the development of post-deployment psychopathology. GR-1F methylation (52 loci) was quantified ... read more using pyrosequencing in whole blood of 92 military men 1 month before and 6 months after a 4-month deployment period to Afghanistan. GR-1F methylation overall (mean methylation and the number of methylated loci) and functional methylation (methylation at loci associated with GR exon 1F expression) measures were examined. We first investigated the effect of exposure to potentially traumatic events during deployment on these measures. Subsequently, changes in GR-1F methylation were related to changes in mental health problems (total Symptom Checklist-90 score) and posttraumatic stress disorder (PTSD) ...
We used differential scanning calorimetry (DSC) and circular dichroism (CD) to investigate thermal unfolding of recombinant fibroblast isoforms of alpha-tropomyosin (Tm) in comparison with that of smooth muscle Tm. These two nonmuscle Tm isoforms 5a and 5b differ internally only by exons 6b/6a, and they both differ from smooth muscle Tm by the N-terminal exon 1b which replaces the muscle-specific exons 1a and 2a. We show that the presence of exon 1b dramatically decreases the measurable calorimetric enthalpy of the thermal unfolding of Tm observed with DSC, although it has no influence on the alpha-helix content of Tm or on the end-to-end interaction between Tm dimers. The results suggest that a significant part of the molecule of fibroblast Tm (but not smooth muscle Tm) unfolds noncooperatively, with the enthalpy no longer visible in the cooperative thermal transitions measured. On the other hand, both DSC and CD studies show that replacement of muscle exons 1a and 2a by nonmuscle exon 1b not ...
To explore exonic variants in possibly associated with gout susceptibility, we sequenced all exons of in 480 gout cases and 480 controls of Japanese male6 and conducted an association analysis (see online supplementary furniture S1 and S2), followed by a replication study on 924 gout instances and 2113 settings (see online supplementary number S1). In two recognized variants with small allele rate of recurrence (MAF) >0.5%, only rs117371763 (c.1129C>T; p.Arg377Cys [R377C]) was significantly associated with gout susceptibility after Bonferroni correction (p=0.014). The significant association between rs117371763 and gout susceptibility was replicated, and our meta-analysis showed a significant protecting effect of rs117371763 on gout susceptibility (OR=0.67; 95% CI 0.53 to 0.85; pmeta=7.810-4) (table 1). In addition, a quantitative trait locus analysis focusing on SUA levels in 3208 individuals (observe online supplementary table S3) showed the small allele of rs117371763 significantly decreases ...
The object isnt able to load since the IDs are different. Same is the case with exons and transcripts ids. Upon looking into the .ctab files, the exons, introns, transcripts differ across Control- Sample. But are same across the 3 controls. And they are same across the 5 samples. It is like so- Controls: exon 442247, introns 366654, transcripts 181466. Samples: exon 686514, introns 416565, transcripts 247538. The exons, introns, transcripts differ only between the two conditions. Hence, I am not able to progress from here. Can anyone please help me with as to why this is occuring? Why would the exons, introns, transcripts id be different for control & sample, since both control and sample RNA are collected from human patients. Please add a note on how I can solve this issue.. Any help is much appreciated.. ...
Four separate CETP gene mutations have been published previously. Of the four mutations, the intron 14 donor splice site mutation4 and the Asp442-to-Gly mutation in exon 1528 are both known to be very common in the Japanese population.7 8 9 10 29 The other two mutations, the Gln309-to-Stop mutation in exon 1026 and a 1-bp insertion in intron 14,7 are probably sporadic mutations. Except for the Asp442-to-Gly mutation that causes partial CETP deficiency, the other three seemed to have null allelic effects, although exact mechanisms underlying the null effects have not been studied. In the present study, we demonstrated that the primary abnormality due to the intron 14 donor splice site mutation is the exon skipping of mRNA, which decreases the level of mRNA and produces a truncated protein that should be degraded intracellularly. These observations clearly explain the molecular basis of the complete CETP deficiency found not only in patients with the common intron 14 splicing mutation but also in ...
Transcription factor binding to enhancer elements is critical for proper gene regulation. Enhancers are often found in noncoding sequences in close proximity to the gene that they regulate and sometimes even on another chromosome; however, whether they are also found in exons, the coding regions of DNA, is unclear. Birnbaum et al. analyzed 25 mouse and human enhancer-associated ChIP-seq data sets in order to identify enhancer peaks that overlap exons and found regulatory transcription factor binding to exonic regions. In fact, in mice, roughly 7% of enhancer peaks overlapped coding exons. Mutation of these elements in zebrafish and mouse enhancer assays showed that although exonic sequences are necessary, they are not sufficient for full enhancer function. Absence of an exon-encoded enhancer, however, did have functional consequences. Thus, exonic sequences may function in the regulation of nearby genes. Moreover, phenotypes seen in genetic knockout animals may be the result of not only the lack ...
Saitta B., Wang Y.-M., Renkart L., Zhang R.-Z., Pan T.-C., Timpl R., Chu M.-L.. The alpha 1(VI) and alpha 2(VI) chains, two of the three constituent chains of type VI collagen, are highly similar in size and domain structure. They are encoded by single-copy genes residing in close proximity on human chromosome 21. To study the evolution of the type VI collagen genes, we have isolated and characterized genomic clones coding for the triple-helical domains of the human alpha 1(VI) and alpha 2(VI) chains, which consist of 336 and 335 amino acid residues, respectively. Nucleotide sequencing indicates that, in both genes, the exons are multiples of 9 bp in length (including 27, 36, 45, 54, 63, and 90 bp) except for those encoding for regions with triple-helical interruptions. In addition, the introns are positioned between complete codons. The most predominant exon size is 63 bp, instead of 54 bp as seen in the fibrillar collagen genes. Of particular interest is the finding that the exon structures of ...
Author(s): Ji, Xinjun; Park, Juw Won; Bahrami-Samani, Emad; Lin, Lan; Duncan-Lewis, Christopher; Pherribo, Gordon; Xing, Yi; Liebhaber, Stephen A | Abstract: Alternative splicing (AS) is a robust generator of mammalian transcriptome complexity. Splice site specification is controlled by interactions of cis-acting determinants on a transcript with specific RNA binding proteins. These interactions are frequently localized to the intronic U-rich polypyrimidine tracts (PPT) located 5 to the majority of splice acceptor junctions. αCPs (also referred to as polyC-binding proteins (PCBPs) and hnRNPEs) comprise a subset of KH-domain proteins with high affinity and specificity for C-rich polypyrimidine motifs. Here, we demonstrate that αCPs promote the splicing of a defined subset of cassette exons via binding to a C-rich subset of polypyrimidine tracts located 5 to the αCP-enhanced exonic segments. This enhancement of splice acceptor activity is linked to interactions of αCPs with the U2 snRNP complex and
The molecular mechanisms of exon definition and back-splicing are fundamental unanswered questions in pre-mRNA splicing. Here we report cryo-electron microscopy structures of the yeast spliceosomal E complex assembled on introns, providing a view of the earliest event in the splicing cycle that commits pre-mRNAs to splicing. The E complex architecture suggests that the same spliceosome can assemble across an exon, and that it either remodels to span an intron for canonical linear splicing (typically on short exons) or catalyses back-splicing to generate circular RNA (on long exons). The model is supported by our experiments, which show that an E complex assembled on the middle exon of yeast EFM5 or HMRA1 can be chased into circular RNA when the exon is sufficiently long. This simple model unifies intron definition, exon definition, and back-splicing through the same spliceosome in all eukaryotes and should inspire experiments in many other systems to understand the mechanism and regulation of ...
How to trace exon number in genome sequence? - posted in Molecular Biology: Hi, I am working on a fusion oncogene (BCR-ABL) causing blood cancer. The problem is that I dont exactly know the product size of my pcr product (amplifying the fusion-oncogene). I know the exons of both genes involved (e13 & 14 of BCR) and (a2 of ABL1) in the chromosomal translocation. but when I try to trace these exons in ensemble sequence I get confused. as there are many small exons not shown i...
This page is badly in need of updating - some of the links are probably broken. A complete redesign wouldnt hurt either. But I have tendonitis, so it wont happen for a while. This is a collection of NPR stories on the Telecommunications bill and Exon Communications Decency Act. These links were organized by me, Steve Rhodes. I have nothing to do with NPR. Im just a listener. You can also listen to the debate on the Senate Floor over Exon and Gingrichs statement against Exon. To listen to any of the audio on this page, you need a free beta verstion of the RealAudio player for the Mac or Windows. There is also more information on Exon. ...
In this study, we demonstrate that Dscam endodomain variants are dynamically and differentially expressed in the developing Drosophila CNS. This conclusion derives from: (1) the analysis of Dscam transcript compositions by RT-PCR, (2) the localization of specific Dscam endodomains by depleting the alternatives via RNAi against exon 19, exon 23, or the unique exon-exon junctions derived from skipping of exon 19 or exon 23 (Fig. 2), and (3) the direct visualization of Dscam+19 using Ab19 as opposed to labeling all the Dscam isoforms with Ab18 (Fig. 3). Postembryonic neuronal morphogenesis uses Dscam variants lacking exons 19 and 23 (Fig. 4C), while Dscam+19 plays a more important role in the wiring of embryonic neural tracts (Fig. 4F). Skipping exon 19 prevents accumulation of Dscams in neuronal cell bodies, implicating a mechanism for regulating Dscam protein targeting by the alternative splicing of exon 19 (Figs. 6, 7). In addition, exon 23 is dispensable for most Dscam-dependent neuronal ...
A fundamental aspect of the independent birth theory is the ability to find complete genes in a string of random DNA in the primordial pond. Because of the length of an average gene, the probability of finding just one unsplit (prokaryote) gene in any amount of DNA is very, very small, even if we consumed all of the mass in the universe when making the DNA. However, when a gene is split into numerous exons, the gene can be found in a far shorter, and very manageable length of random DNA. In fact, almost any gene can be found in a small amount of random DNA -- if the gene is split into exons. [Reference: Independent Birth of Organisms, Chapter 7, pages 223 - 253]. Furthermore, because of codon and amino acid degeneracies, the probability of finding a split gene that codes for a particular protein function is even higher in a reasonable amount of DNA. [Reference: pages 254 - 266]. This search engine demonstrates how easily a complete gene composed of exons (or words) can be found in a random ...
Exon Property Pte Ltd, a franchisee of Century 21 Singapore, is set by its Key Executive Officer (KEO), Eddy Lau.. Eddy Lau started his real estate career in 1993, from an associate realtor to associate director within a short period of 2 years. As a veteran in the real estate industry for over the last 2 decades, he won numerous top achiever award from various real estate agencies before setting up Exon Property Pte Ltd.. All salespersons in Exon Property have at least 3 years of experience is real estate. And our international project team, set up in the year 2008, has successfully marketed properties from Malaysia, Thailand, UK, USA & Australia across to investors in the region.. Today, as CENTURY 21 Exon Property Pte Ltd, we are part of the largest real estate sales organisation in the world.. ...
In the current study, we report on differences in outcome based on EGFR genotype after treatment with gefitinib or erlotinib in patients with NSCLC. A total of 36 eligible patients with EGFR mutations were identified. Of these, 32 (89%) patients had either an exon 19 deletion (n = 22) or the L858R point mutation (n = 10). This is the second study to compare patients with exon 19 deletions with those harboring an L858R point mutation and provides important independent validation to earlier observations (35). In a previously reported study, Riely et al. analyzed 34 NSCLC patients with either an exon 19 deletion (n = 23) or an L858R mutation (n = 11). Of these, 22 were treated with gefitinib and 12 were treated with erlotinib. The baseline characteristics of the patients in both studies are remarkably similar with respect to age, gender, smoking status, tumor histology, performance status, number of prior chemotherapy regimens, and EGFR-TKI administered.. Although the radiographic response rate in ...
Objective The innate immune component TRIM5α has the ability to restrict retrovirus infection in a species-specific manner. TRIM5α of some primate species restricts infection by HIV-1, while huTRIM5α lacks this specificity. Previous studies have suggested that certain polymorphisms in huTRIM5 may enhance or impair the proteins affinity for HIV-1. This study investigates the role of TRIM5 polymorphisms in resistance/susceptibility to HIV-1 within the Pumwani sex worker cohort in Nairobi, Kenya. A group of women within this cohort remain HIV-1 seronegative and PCR negative despite repeated exposure to HIV-1 through active sex work. Design A 1 kb fragment of Trim5alpha gene, including exon 2, from 1032 women enrolled in the Pumwani sex worker cohort was amplified and sequenced. SNPs and haplotypes were compared between HIV-1 positive and resistant women. Methods The TRIM5 exon 2 genomic fragment was amplified, sequenced and genotyped. Pypop32-0.6.0 was used to determine SNP and haplotype ...
MAGOH (mago homolog, exon junction complex core component), Authors: Dessen P. Published in: Atlas Genet Cytogenet Oncol Haematol.
For each BAM, we use samtools to retrieve the reads in the region(s)) of interest. The reads are then filtered with samjs (https://github.com/lindenb/jvarkit/wiki/SamJS) to only keep the reads carrying an intron-exon junction at the desired location(s). Basically, the javascript-based filter loops over the CIGAR string of the read, computes the genomic interval skipped when the cigar operator is a deletion or a skipped region/intron. The read is printed if it describes the new intron-exon junction ...
Gene identification studies, centred on a region of overlapping loss of heterozygosity in breast tumours within band 1p31.1, lead to the characterisation of LPHH1, a novel human 7TM gene. The coding sequence of LPHH1 extends over a 60 kb region and comprises in excess of 28 exons. Alternative splicing occurs minimally at five positions, four of which are within the coding sequence. The fifth region of alternative splicing occurs at the extreme 5 end of the transcript. A clear tissue specific bias in alternative exon selection is observed to some degree at all five positions, including the extreme 5 region, which raises the possibility of multiple and perhaps tissue specific promoters. One such putative promoter region, which appears to be utilised predominantly in breast cancer cells, has been identified. LPHH1 is highly evolutionarily conserved, with the simplest (19 exon) gene product being 95% identical between human and rat. Comparison of the alternatively spliced exons between three ...
Data_Sheet_2_Widespread Separation of the Polypyrimidine Tract From 3′ AG by G Tracts in Association With Alternative Exons in Metazoa and Plants.zip
Data_Sheet_1_Widespread Separation of the Polypyrimidine Tract From 3′ AG by G Tracts in Association With Alternative Exons in Metazoa and Plants.zip
RosBREEDSNP_SNP_AC_27071636_Lg15_02084_MAF30_187884_exon1, RosBREEDSNP_SNP_AC_27071636_Lg15_02084_MAF30_187884_exon1 (genetic_marker) Malus x ...
RosBREEDSNP_SNP_TC_45022535_Lg15_ACS_MAF50_1618441_exon1, RosBREEDSNP_SNP_TC_45022535_Lg15_ACS_MAF50_1618441_exon1 (genetic_marker) Malus x ...
Background: CD36 is a multiligand receptor involved in various metabolic pathways, including cellular uptake of long-chain fatty acids. Defect function or expression of CD36 can result in dyslipidemia or insulin resistance. We have previously shown that CD36 expression is female-predominant in rat liver. In the present study, hormonal and nutritional regulation of hepatic CD36 expression was examined in male and female rats. Since alternative transcription start sites have been described in murine and human Cd36, we investigated whether alternative CD36 transcripts are differentially regulated in rat liver during these conditions.. Results: Sequence information of the rat Cd36 5-UTR was extended, showing that the gene structure of Cd36 in rat is similar to that previously described in mouse with at least two alternative first exons. The rat Cd36 exon 1a promoter was sequenced and found to be highly similar to murine and human Cd36. We show that alternative first exon usage is involved in the ...
Fig. 4 shows the amino acid sequences of the predicted proteins of AtFpg-1, -1a, -2, -3, and -4. Exons 1, 2, 3, 5, 6, and 7 were entirely conserved in all the Arabidopsis cDNA clones. The polypeptide chains encoded by exons 1, 5, 6,and 7 represent the major conserved regions between Arabidopsis and bacterial FPGs , showing between 29 and 54% identity between Arabidopsis and E. coli amino acid sequences. The N-terminal sequence of exon 1 and the lysine of exon 5 (K155) of E. coli FPG have been associated with the active site. The predicted amino acid sequence coded by exon 1 shows a surprising relationship to a sequence from DNA photolyase, another DNA repair enzyme but one quite unrelated to FPG (Fig. 5). If this relates to DNA binding, it might explain how AtFPG-2, which lacks the C-terminal DNA-binding region present in AtFPG-1 (or the zinc-finger of E. coli FPG) might have the DNA cleavage activities measured by Gao and Murphy (Photochem. Photobiol., in press). The optional exons are exon 4 ...
Recent studies suggest that ANRIL expression mediates susceptibility to CAD1 via CDKN2B.2 We used fluorescently-labelled whole-blood RNA, from 20 healthy volunteers genotyped for the CAD-risk-SNP rs2891168, to probe custom-designed Agilent tiling expression microarrays. Raw data were normalized to probe GC content and housekeeping genes. We found that ANRIL exons 1-4 were more abundantly expressed in blood than 5-20, with exons 6, 8, 9, 20 showing low expression. We derived a set of training tiling probes from HUVEC cells in which ANRIL expression was attenuated using siRNA against exons 13 and 19. ANRIL expression (probes in exons 5,6,8,13,16,18,19) was reduced by at least 50% and CDKN2B expression (probes in exons 1,2) increased, with no effect on CDKN2A. We confirmed these data using real-time QPCR. Using the tiling probe training-set, a probe in exon 16 of ANRIL showed a CAD genotype-specific difference in expression (p,0.001), with the risk-allele lower, and probes in exon 2 of CDKN2B ...
This gene is a member of the protocadherin alpha gene cluster, one of three related gene clusters tandemly linked on chromosome five that demonstrate an unusual genomic organization similar to that of B-cell and T-cell receptor gene clusters. The alpha gene cluster is composed of 15 cadherin superfamily genes related to the mouse CNR genes and consists of 13 highly similar and 2 more distantly related coding sequences. The tandem array of 15 N-terminal exons, or variable exons, are followed by downstream C-terminal exons, or constant exons, which are shared by all genes in the cluster. The large, uninterrupted N-terminal exons each encode six cadherin ectodomains while the C-terminal exons encode the cytoplasmic domain. These neural cadherin-like cell adhesion proteins are integral plasma membrane proteins that most likely play a critical role in the establishment and function of specific cell-cell connections in the brain. Alternative splicing has been observed and additional variants have been ...
This gene is a member of the protocadherin alpha gene cluster, one of three related gene clusters tandemly linked on chromosome five that demonstrate an unusual genomic organization similar to that of B-cell and T-cell receptor gene clusters. The alpha gene cluster is composed of 15 cadherin superfamily genes related to the mouse CNR genes and consists of 13 highly similar and 2 more distantly related coding sequences. The tandem array of 15 N-terminal exons, or variable exons, are followed by downstream C-terminal exons, or constant exons, which are shared by all genes in the cluster. The large, uninterrupted N-terminal exons each encode six cadherin ectodomains while the C-terminal exons encode the cytoplasmic domain. These neural cadherin-like cell adhesion proteins are integral plasma membrane proteins that most likely play a critical role in the establishment and function of specific cell-cell connections in the brain. Alternative splicing has been observed and additional variants have been ...
By means of alternative splicing in two of its nine exons (exons 3 and 6), the RDL gene encodes four distinct polypeptides (Fig. 1A), all of which are expressed (ffrench-Constant and Rocheleau, 1993). Three splice variants (RDLac, RDLbd, and RDLab) have been cloned and functionally expressed (Hosie and Sattelle, 1996a). Residues that vary in exon 3 lie upstream to loop D of the GABA binding site and near the equivalent positions of known determinants of agonist potency in GABAA receptors of vertebrates. Alternative splicing occurs in other ligand-gated ion channels (Villarroel, 1999) and has been shown to affect agonist sensitivity in glycine receptors (Miller et al., 2004). It is noteworthy that alternative splicing of the D. melanogaster nicotinic acetylcholine receptor subunit Dα6 (Grauso et al., 2002) also occurs in exon 3, which aligns to exon 3 of RDL. The exon 6 alternatively spliced residues of RDL lie in loops F and C (Fig. 1B) and exon 6 splicing affects the expressed receptors ...
This gene is a member of the protocadherin alpha gene cluster, one of three related gene clusters tandemly linked on chromosome five that demonstrate an unusual genomic organization similar to that of B-cell and T-cell receptor gene clusters. The alpha gene cluster is composed of 15 cadherin superfamily genes related to the mouse CNR genes and consists of 13 highly similar and 2 more distantly related coding sequences. The tandem array of 15 N-terminal exons, or variable exons, are followed by downstream C-terminal exons, or constant exons, which are shared by all genes in the cluster. The large, uninterrupted N-terminal exons each encode six cadherin ectodomains while the C-terminal exons encode the cytoplasmic domain. These neural cadherin-like cell adhesion proteins are integral plasma membrane proteins that most likely play a critical role in the establishment and function of specific cell-cell connections in the brain. Alternative splicing has been observed and additional variants have been ...
We read with great interest the recent paper by Beer and Sahin-Tóth1 addressing the missing heritability observed in approximately 60% of German cases of chronic pancreatitis.2 These authors opined that discovery studies tend to focus on exons and exon-intron boundaries and may thus miss many intronic variants.1 This premise seems eminently reasonable, given the generally much larger size of intronic sequences as compared with the coding sequences of protein-coding genes. However, there is a trade-off here. On the one hand, larger sequence size means larger target size for mutation, and hence the greater the number of mutations that could be missed if intronic sequences were not screened. On the other hand, to be of pathological significance, an intronic mutation must either create a new functional splicing donor or acceptor site or alternatively impact a functional sequence motif responsible for regulating splicing (eg, an intronic splicing enhancer), which depends upon many additional ...
This study demonstrates that some FTDP-17 mutations alter the MT-binding properties of tau, and others alter the ratio of 4R/3R tau isoforms. Intronic mutations (for example, in the DDPAC kindred) presumably alter 4R/3R tau ratios by weakening a stem-loop structure at the 5′ splice site of exon 10, which normally inhibits the inclusion of exon 10 into tau mRNA (5). How the N279K mutation increases 4Rtau production is less clear. Because the N279K mutation does not alter the binding of tau to MTs or decrease the ability of tau to promote MT assembly, the selective aggregation of 4Rtau into filamentous lesions probably results from overproduction of 4Rtau proteins by increasing the inclusion of exon 10 into more tau mRNAs. Presumably, this mutation could act by altering an exon-splicing enhancer (ESE) sequence in exon 10 (15). At the nucleotide level, the N279K mutation changes the normal sequence of TAAGAA to GAAGAA, a potential GAR (where R is a purine) ESE motif (6). These ESE sequences have ...
Alternative Isoform Detection Using Exon Arrays: 10.4018/978-1-60566-076-9.ch015: Eukaryotic genes have the ability to produce several distinct products from a single genomic locus. Recent developments in microarray technology allow
Methods. The human GNB1 locus extends from base 1812355 (5 end) to 1706589 (3 end) in the genomic sequence of chromosome 1p (NCBI). The gene has 12 exons. There is an open reading frame in exons 3 to 11 with a coding sequence corresponding to the human cDNA sequence of the β-subunit of rod transducin (accession number BC004186) [6]. This human cDNA sequence encodes a polypeptide with a sequence identical to the β-subunit of rod transducin in both cattle (accession number BC105260) and mice (accession number NM_008142) [5-7]. We developed PCR-based methods to amplify individually each of the 12 exons of the human GNB1 gene. The primers used for PCR are in Table 1. Each set of primers amplified an entire exon as well as 10 to 72 bp of flanking intron DNA or untranslated region. We amplified the individual exonic fragments from genomic leukocyte DNA from 185 unrelated patients with ADRP. These patients came from families with at least two affected generations with RP; many families had three or ...
The CD19 antigen, expressed on most B-cell acute lymphoblastic leukemias (B-ALL), can be targeted with chimeric antigen receptor-armed T cells (CART-19), but relapses with epitope loss occur in 10% to 20% of pediatric responders. We detected hemizygous deletions spanning the CD19 locus and de novo frameshift and missense mutations in exon 2 of CD19 in some relapse samples. However, we also discovered alternatively spliced CD19 mRNA species, including one lacking exon 2. Pull-down/siRNA experiments identified SRSF3 as a splicing factor involved in exon 2 retention, and its levels were lower in relapsed B-ALL. Using genome editing, we demonstrated that exon 2 skipping bypasses exon 2 mutations in B-ALL cells and allows expression of the N-terminally truncated CD19 variant, which fails to trigger killing by CART-19 but partly rescues defects associated with CD19 loss. Thus, this mechanism of resistance is based on a combination of deleterious mutations and ensuing selection for alternatively ...
flataustralia posted a photo of the new Colony Exon flatland tires. As you can clearly see the maximum pressure is 110 PSI and there was probably no way to write that even bigger ;-) They come as 20 x 1.75 and should be a great addition to the Colony Exon flatland range. More details are yet to be announced ...
Sen. J. James Exon (D-Neb.), 63, has been hospitalized after complaining of stomach pains, his office said today.Mark Bowen, Exons press secretary, said doctors at Bethesda Naval Hospital have
Lynch syndrome patients are susceptible to colorectal and endometrial cancers owing to inactivating germline mutations in mismatch repair genes, including MSH2 (ref. 1). Here we describe patients from Dutch and Chinese families with MSH2-deficient tumors carrying heterozygous germline deletions of the last exons of TACSTD1, a gene directly upstream of MSH2 encoding Ep-CAM. Due to these deletions, transcription of TACSTD1 extends into MSH2. The MSH2 promoter in cis with the deletion is methylated in Ep-CAM positive but not in Ep-CAM negative normal tissues, thus revealing a correlation between activity of the mutated TACSTD1 allele and epigenetic inactivation of the corresponding MSH2 allele. Gene silencing by transcriptional read-through of a neighboring gene in either sense, as demonstrated here, or antisense direction, could represent a general mutational mechanism. Depending on the expression pattern of the neighboring gene that lacks its normal polyadenylation signal, this may cause either
Schramm, A, Schowe, B, Fielitz, K, Heilmann, M, Martin, M, Marschall, T, … Schulte, J.H. (2012). Exon-level expression analyses identify MYCN and NTRK1 as major determinants of alternative exon usage and robustly predict primary neuroblastoma outcome. British Journal of Cancer, 107, 1409-1417 ...
Embryonic, larval, and pupal Antp RNA products of 3.5 and 5kb can be detected. Antennapedia is transcribed from two promoters (P1 and P2) but at least it was not clear in the past whether the protein is produced from P2 transcript (Laughon et al., (1986)). GI:156946 was not studied by IRESite curator in detail yet. The transcript from the P1 promoter has 1512nt long 5-UTR derived from non-coding exons A (55nt), B(88nt), D(252nt), E (621 out of 777nt are coding) and from coding exons F(39nt), G(226nt), H(819nt; note the difference to the H exon of P2 variant below). P1 transcripts are of 3.4 and 4.9kb and appear slightly later than the exon C transcripts (from promoter P2). The 4.9-kb RNA is more abundant than the 3.4-kb species in embryos. Antp transcripts are also found in third-instar larvae and in pupae at about 1/10 of the embryonic levels (Laughon et al., (1986) Fig. 2A). [Laughon et al., (1986)] P1 related GenBank records: complete P1 mRNA record GI:156948, 4694nt long, CDS[1526-2662] DNA ...
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): ...
... comprises four exons. Five TMEM125 promoters were identified by Genomatix Gene2Promoter. The primary promoter (NM_ ...
... 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 ...
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. ...
It contains twenty exons. Hel308's principal role is to repair replication-blocking lesions, such as interstrand DNA cross- ...
It contains 7 exons. The protein encoded by this gene contains 410 amino acids, and forms a homodimer with another chain. The ...
... is located at 15q21.3 and has 18 exons. However, some exons overlap; therefore, there are only 13 distinguishable exons in ...
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 ...
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 ...
COMP contains 19 exons. The cartilage oligomeric matrix protein is 757 aa (OMIM 2008). COMP protein is found in the ...
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 ...
It contains 18 exons. The protein encoded by this gene contains 258 amino acids, and forms a homodimer with another chain. Its ...
It contains 19 exons. GLS2 is a part of the glutaminase family. The protein encoded by this gene is a mitochondrial phosphate- ...
... might define exons. Nucleosomes in the exons have more histone modifications such as H3K79, H4K20, and especially ...
It has 9 exons. The transcript of the gene is about 5000kB long, as determined through utilization of northern blot techniques ...
It contains five exons. There is not a consensus on whether humans have one or two SKIDA1 isoforms. NCBI Gene claims there is ...
TMEM53 has 3 exons. Twelve alternative splice forms have been identified using 26 alternative exons. The following table ...
LGALS1 contains four exons. The galectin-1 protein is 135 amino acids in length and highly conserved across species. It can be ...
The reference isoform does not include exon 2 and isoform X1 does not include exon 1. SBK3's reference protein has a predicted ... SBK3 has five exons; however, only four are included in the final mRNA transcript. SBK3 is found to have one isoform outside of ...
"Greyson Lambert goes 24/25 (96 percent) to set NCAA accuracy record". EXON. Retrieved 19 September 2015. "2011 Football ...
Exon. & alios Regis Justiciarios ad Fratres Praedicatores tunc congregatos ("The Bishops of London and Exeter and other ...
Exon. p. 318. Davis, Robert. Christian Slaves, Muslim Masters: White Slavery in the Mediterranean, the Barbary Coast, and Italy ...
Exon. Page 146 Both as Members of Parliament for Plympton Erle and Devon and as Sheriff of Devon Greenway Fasti Ecclesiae ... Bishop of Exon". The blazon contravenes the heraldic "Rule of Tinctures" Denton "Bronescombe, Walter of" Oxford Dictionary of ...
Exon. https://www.exeter.ox.ac.uk/wp-content/uploads/2019/10/exon-19.pdf.CS1 maint: location (link) "Agent 160 Theatre Company ...
The gene contains 17 exons. HADHB encodes a 51.2 kDa protein that is composed of 474 amino acids; 124 peptides have been ...
The gene holds 9 exons. The most common variant of mRNAs of CFAP157 contains 1,722 base pairs. CFAP157 is expressed in many ...
Both exons are usually transcribed. A few cases exist where only the second exon was transcribed. A fusion transcript ... The translational start site of C1orf74 is after the exon-exon junction, which means the protein is made only by translating ... The transcript contains two exons and one upstream in-frame stop codon. The 5' UTR of this transcript is 343 nucleotides long ... The gene contains two exons. C1orf74 is downstream of the gene interferon regulatory factor 6 or IRF6 in humans. C1orf74 is ...
DUX4 consists of three exons. Exons 1 and 2 are in each repeat. Exon 3 is in the pLAM region telomeric to the last partial ...
Exon 2 contains the junction of the membrane-binding domain and the catalytic domain of b5R, which shows that there are two ... The gene contains 12 exons. CYB5R3 encodes a 34.2 kDa protein that is composed of 301 amino acids; 63 peptides have been ... gene encodes both forms of the enzyme which arise from tissue-specific alternative transcripts that differ in the first exon. ...
The gene has 10 exons. The HADH gene encodes a 34.3 kDa protein that has 314 amino acids and 124 observed peptides. This gene ...
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 ... A single-nucleotide exon has been reported from the Arabidopsis genome. In protein-coding genes, the exons include both the ... Exon trapping or gene trapping is a molecular biology technique that exploits the existence of the intron-exon splicing to ...
Exon may refer to: Exon, a region of DNA that is represented in the mature form of RNA Exoribonuclease or ExoN, an RNA ... James Exon (1921-2005), American politician Nat Exon (born 1992), Australian rules footballer Exon is a rank for an officer in ... degrading enzyme Exoniensis or Exon., the Post-Nominal Letters for alumni / degrees from the University of Exeter Exon can also ... a brand of fuel sold by ExxonMobil This disambiguation page lists articles associated with the title Exon. If an internal link ...
... or the same exon can be duplicated, to create a new exon-intron structure.[1] 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 ... Therefore, exon shuffling became a major role in the construction of younger proteins.[citation needed] ... In order for exon shuffling to start to play a major role in protein evolution the appearance of spliceosomal introns had to ...
Deciphera Pharmaceuticals, Inc., a clinical-stage biopharmaceutical company focused on addressing key mechanisms of tumor drug resistance, announced the presentation today of updated preliminary results from its ongoing Phase 1 clinical study of DCC-2618, the companys broad-spectrum KIT and PDGFRα inhibitor, in patients with gastrointestinal stromal tumors as a proffered paper presentation at the European Society of Medical Oncology 2018 Congress in Munich, Germany.. ...
... the accurate identification of short exons remains a challenging problem. In this paper... ... the accurate identification of short exons remains a challenging problem. In this paper we concentrate on short initial exons ... Donor Site Gene Prediction Computational Identification Translation Initiation Site Internal Exon These keywords were added by ... The algorithm was evaluated on a total of 158 sequences containing short initial exons, and achieves an accuracy of up to 73%. ...
John James Exon, J. James Exon, Jim Exon (ur. 9 sierpnia 1921 w Geddes, Dakota Południowa, zm. 10 czerwca 2005 w Lincoln, ... Źródło: „https://pl.wikipedia.org/w/index.php?title=James_Exon&oldid=49262054" ...
But how do I sort within genes? That is, how do I get the top 2 exons per gene (highest expressing exons per gene) and, if ... An additional nicety would be to somehow work in a preference for 5 exons. For example, lets say a gene has 3 exons and, with ... Id like to selectively get the first 2 exons. Ive started learning Galaxy and was able to import BED files for UCSC exons (as ... galaxy-user] Constitutive exon workflow? 7plusorminus 3 Mon, 10 Feb 2014 02:01:25 -0800 ...
Jim Exon. Politician (9-Aug-1921 10-Jun-2005). SUBJECT OF BOOKS. We do not have any books for this individual listed. If you ...
Is there any way of finding out where the intron/exon (exon-exon) boundaries are in a cDNA sequence? I am trying to design PCR ... Introns and Exons again.... Dr. N.A. Affara naffara at crc.ac.uk Wed Oct 7 10:19:36 EST 1992 *Previous message: Automated ... but not much about average length of introns and exons. Thanks very much if you have replied already! Phil (E-mail naffara at ...
Affymetrix exon array. Tag archives for Affymetrix exon array. Dont Throw Out Those Introns. Posted by weizmann science writer ...
Exons press secretary, said doctors at Bethesda Naval Hospital have ... J. James Exon (D-Neb.), 63, has been hospitalized after complaining of stomach pains, his office said today.Mark Bowen, ... Mark Bowen, Exons press secretary, said doctors at Bethesda Naval Hospital have diagnosed the pains as "relating to the ... J. James Exon (D-Neb.), 63, has been hospitalized after complaining of stomach pains, his office said today. ...
Exon Nation was founded by Exon Tray(Trayshawn Gillis) in May 18, 2015. ... Exon Nation has been around since 2015 competing in online and travel tournaments on GameBattles and CWL LAN tournaments ... and Mixer streamers that broadcast their self-live to hundredths of their followers and rep Exon Nation in there live streams ... Exon Nation is a professional Gaming Organization, which focuses mainly on eSports and Content Creation in Call of Duty, ...
... Shengxian Wang shen at CUBSPS.BIO.COLUMBIA.EDU Wed Feb 5 22:36:35 EST 1997 *Previous message: Fly feeding ... exon) resides in another genes intron region. I heard of examples, but would like to have a few papers to look at. Could ...
... collaborative research team including Senior Researcher Yun Ha Jeong succeeded in discovering a phenomenon that cryptic exons ... IMAGE: (a) While some cryptic exons are common between cell types, many cryptic exons are unique to neurons (58), muscle (79) ... Cryptic exons are regions of the genome that are normally skipped by the spliceosome due to the presence of adjacent UG ... If Tdp-43 is normal, it will repress the expression of a specific cryptic exon and produce a normal protein; however, when a ...
The CDS feature changes to exon (the third column, type.). Advertising. Is it a bug or done on purpose? I have Artemis version ... Hi! A gff3 file contains features of gene, mRNA, exon and CDS. When I opened such a gff3 file in Artemis, and save out the gff3 ... Artemis-users] CDS changed to exon in gff3 Feifei Xu Wed, 21 Sep 2011 02:46:59 -0700 ...
Human Exon 1.0 ST Array Sample Data Update *changed the chiptype setting in the CEL files from HuEx-1_0-st-v1 to HuEx-1_0-st-v2 ... January 15, 2006 Human Exon 1.0 ST Array Update Notes. Updated the design time annotations based on some improvements and bug ... This field is set with the transcript_cluster_id, not exon level probe set id. This change makes it easier to merge these ... These changes affect some of the transcript cluster and exon cluster IDs. They also affect transcript cluster groupings. New ...
Jim Exon on other issues:. NE Gubernatorial:. Mike Johanns. NE Senatorial:. Ben Nelson. Bob Kerrey. Charlie Matulka. Chuck ... Click here for SenateMatch answers by Jim Exon. *Agree? Disagree? Voice your opinions on Environment in The Forum. ... Jim Exon on Environment Voted YES on continuing desert protection in California. Invoking cloture on the California desert ...
The average exon encoded 30-36 amino acids.[6] While the longest exon in the human genome is 11555 bp long, several exons have ... The first exon of a trapped gene splices into the exon that is contained in the insertional DNA. This new exon contains the ... For other uses, see Exon (disambiguation).. An exon is any part of a gene that will encode a part of the final mature RNA ... Experimental approaches using exonsEdit. Exon trapping or gene trapping is a molecular biology technique that exploits the ...
... Date: Fri May 5 16:40:29 2000. Posted By: Gabriel Vargas M.D.,Ph.D ... In contrast, exons are the sequences within a gene which do get expressed and translated into protein. Intergenic DNA, as the ...
Authoritative and practical Exon Skipping: Methods and Protocols seeks to aid scientists in the continuing study of exon ... Exon Skipping. Book Subtitle. Methods and Protocols. Editors. * Annemieke Aartsma-Rus Series Title. Methods in Molecular ... Exon Skipping: Methods and Protocols provides scientist with a comprehensive guide to many of the methods and techniques used ... To functionally test these a lot can be achieved with a limited set of protocols, while for the intentional induction of exon ...
Target Exon - Those who dismiss global warmings threat have embraced a series of arguments, retreating from one to the next as ... Target Global Warming, Target Exon. By Paul Rogat Loeb (Page 1 of 2 pages) (View How Many People Read This) 3 comments ... Related Topic(s): Corporation Exon Mobile; Global Warming, Add Tags. Add to My Group(s) ...
Jim Exon on other issues:. NE Gubernatorial:. Mike Johanns. NE Senatorial:. Ben Nelson. Bob Kerrey. Charlie Matulka. Chuck ... Click here for SenateMatch answers by Jim Exon. *Agree? Disagree? Voice your opinions on Foreign Policy in The Forum. ... Jim Exon on Foreign Policy Voted YES on Strengthening of the trade embargo against Cuba. Strengthening of the trade embargo ...
On the issues: Jim Exon Senate Match , NE Governor: Mike Johanns Nebraska Senators: Ben Nelson Bob Kerrey Charlie Matulka Chuck ... Jim Exon is a Moderate Populist Conservative. Click here for explanation of political philosophy. Click here for VoteMatch quiz ... Jim Exon on Energy & Oil Click here for the full quote on Energy & Oil OR background on Energy & Oil. *Voted YES on do not ... Jim Exon on Free Trade Click here for the full quote on Free Trade OR background on Free Trade. *Voted YES on imposing trade ...
... does not hold a share or financial interest in this hospital, another Nuffield Health hospital or the company. ... Mr David Exon does not have a share or financial interest in equipment used at this hospital or another Nuffield Health ... Mr David Exon does not hold any paid advisory role(s) at this hospital or on behalf of Nuffield Health. ... David Exon was appointed as Consultant Upper GI & General Surgeon in Leicester in 2010. Originally from Birmingham, he studied ...
... or the same exon can be duplicated, to create a new exon-intron structure.[1] 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 ... In order for exon shuffling to start to play a major role in protein evolution the appearance of spliceosomal introns had to ... Exon shuffling follows certain splice frame rules. Introns can interrupt the reading frame of a gene by inserting a sequence ...
One in exon 4 substituting leucine with phenylalanine (L84F) in a familial patient and the second in exon 3 at substituting ... Mutations in all five exons of SOD-1 may cause ALS.. Shaw CE1, Enayat ZE, Chioza BA, Al-Chalabi A, Radunovic A, Powell JF, ... Over 60 point mutations have now been described in all five exons of SOD-1, involving 43 of the 153 residues. Hypotheses about ...
Saturation Editing of BRCA1 Exons Reveals Functional, Non-Functional Variants. Sep 12, 2018 ...
The theory that exons are basic modules of protein structure that can be shuffled by evolution (much like DNA shuffling, ... EXON 1 ,_______, NEW EXON ,_________, EXON 2 ,________ ,___________, INT ,_____________, RON ,_____________, Arguments tend to ... exon shuffling (idea). See all of exon shuffling, no other writeups in this node. ... The theory that exons are basic modules of protein structure that can be shuffled by evolution (much like artificial methods). ...
Distance-Dependent Processing of Adeno-Associated Virus Type 5 RNA Is Controlled by 5′ Exon Definition Jianming Qiu, Fang Cheng ... Exon 3 of the Human Cytomegalovirus Major Immediate-Early Region Is Required for Efficient Viral Gene Expression and for ... The DR1 and DR6 First Exons of Human Herpesvirus 6A Are Not Required for Virus Replication in Culture and Are Deleted in Virus ... Splicing Regulatory Elements within tat Exon 2 of Human Immunodeficiency Virus Type 1 (HIV-1) Are Characteristic of Group M but ...
Absence of an exon-encoded enhancer, however, did have functional consequences. Thus, exonic sequences may function in the ... In fact, in mice, roughly 7% of enhancer peaks overlapped coding exons. Mutation of these elements in zebrafish and mouse ... whether they are also found in exons, the coding regions of DNA, is unclear. Birnbaum et al. analyzed 25 mouse and human ... of the deleted gene but also alterations in the expression of genes that are regulated by enhancers in the deleted exons. ...
  • Introns and Exons again. (bio.net)
  • but not much about average length of introns and exons. (bio.net)
  • Re: What is intergenic DNA compared to introns and exons? (madsci.org)
  • Also I suppose that if it is the complete sequence it contains the introns and exons from each chromosome, is there any site where I can download only the exons or the introns of each chromosome? (protocol-online.org)
  • how do I find the introns and exons? (protocol-online.org)
  • I have clicked on just about everything there is to click on, but I can't come up with the introns and exons in NCBI. (protocol-online.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)
  • It is a process through which two or more exons from different genes can be brought together ectopically , or the same exon can be duplicated, to create a new exon-intron structure. (wikipedia.org)
  • What is clear now is that the eukaryotic exon-intron structure is not static, introns are continually inserted and removed from genes and the evolution of introns evolves parallel to exon shuffling. (wikipedia.org)
  • Is there any way of finding out where the intron/exon (exon-exon) boundaries are in a cDNA sequence? (bio.net)
  • Dear fly people: I have been trying to find some references about the cases in Drosophila in which one gene's coding sequence (exon) resides in another gene's intron region. (bio.net)
  • Intron and exon classes. (wikipedia.org)
  • I don't know why they think that the 1st intron comes before the 1st exon. (studentdoctor.net)
  • Sinon cet intron non episs va provoquer l'arret de la traduction (a moins qu'il soit en phase? (futura-sciences.com)
  • A very large number of intron/exon junctions have been determined -- a single issue of Genomics alone contains many dozens of new ones. (mad-cow.org)
  • Specialized online software has been developed to detect valid exon-intron boundaries: human exon 2 is affirmed by caomparisons and these methods. (mad-cow.org)
  • B. Draw a picture of YFG's most likely intron/exon organization. (biology-online.org)
  • I have also attached a picture of how I would draw YFG's intron/exon organization. (biology-online.org)
  • The gene is transcribed from left (5′) to right (3′) beginning at the promoter (P). The long primary RNA transcript contains both intron and exon sequences. (blogspot.com)
  • The cell must cleave the primary transcript at each end of the intron while holding on to the flanking exons so the chopped RNA transcript does not come apart. (blogspot.com)
  • This results in cleavage of the 3′ intron/exon junction and joining of the 5′ exon to the 3′ exon. (blogspot.com)
  • 14 /note='intron III (1.1 kb)' exon 15. (davidson.edu)
  • 144 /note='calcium-binding protein (exon 4) (aa 62-105) (15 is 2nd base in codon) (144 is 2nd base in codon)' /usedin=X03287:cbin_cds intron 145. (davidson.edu)
  • Using intron-based exon-specific primers, we amplified exons 23-32 from genomic DNAs, screened these fragments by single-stranded conformational polymorphism analysis, and sequenced indicated exons. (osti.gov)
  • Exonization is the creation of a new exon, as a result of mutations in introns. (wikipedia.org)
  • This will reveal many mutations that potentially lead to exon skipping. (springer.com)
  • Exon Skipping: Methods and Protocols provides scientist with a comprehensive guide to many of the methods and techniques used for exon skipping, such as methods on how to discriminate "real polymorphisms" from mutations that affect splicing. (springer.com)
  • Mutations in all five exons of SOD-1 may cause ALS. (nih.gov)
  • Over 60 point mutations have now been described in all five exons of SOD-1, involving 43 of the 153 residues. (nih.gov)
  • We now need to address the impact of mutations that affect the splicing process, as their consequences could vary from the activation of cryptic signals to the skipping of one or multiple exons. (nih.gov)
  • Despite the major developments of the bioinformatics field coupled to experimental data generated on splicing, it is today still not possible to efficiently predict the consequences of mutations impacting splicing signals, especially to predict if they will lead to exon skipping or to cryptic splice site activation. (nih.gov)
  • NPM exon 12 mutations are AML-specific since they are not detected in normal cells or other neoplasms. (questdiagnostics.com)
  • The mystery of exon 2 is why the sequence is so conserved when the uses of it seem minor if not obscure: how can exon 2 be so important that accepted point mutations are rare when the ORF itself can be knocked out without dramatic consequences? (mad-cow.org)
  • Rare mutations or de novo mutations in critical exons should be scrutinized further. (sciencemag.org)
  • Select brain-expressed exons may be targets for disease-causing mutations in autism. (sciencemag.org)
  • Exon skipping by ASOs is gaining traction as a therapeutic strategy, and the use of ASOs is now being applied to bypass mutations and generate modified but functional proteins for an array of genetic disorders. (jci.org)
  • This strategy would treat laminopathies due to mutations in exon 11 and 12. (jci.org)
  • Aartsma-Rus A, Fokkema I, Verschuuren J, Ginjaar I, van Deutekom J, van Ommen GJ: Theoretic applicability of antisense-mediated exon skipping for Duchenne muscular dystrophy mutations. (springer.com)
  • The condition is the result of mutations in FBN1, a large gene composed of 65 exons encoding the fibrillin-1 protein. (osti.gov)
  • While mutations causing classic manifestations of Marfan syndrome have been identified throughout the FBN1 gene, the six previously characterized mutations resulting in the severe, perinatal lethal form of Marfan syndrome have clustered in exons 24-32 of the gene. (osti.gov)
  • This analysis documented mutations in exons 25-27 of the FBN1 mutations in 6 of these patients. (osti.gov)
  • These results, taken together with previously published FBN1 mutations in this region, further define the phenotype associated with mutations in exons 24-32 of the FBN1 gene, information important for the development of possible diagnostic tests and genetic counseling. (osti.gov)
  • Just as the entire set of genes for a species constitutes the genome, the entire set of exons constitutes the exome. (wikipedia.org)
  • Across all eukaryotic genes in GenBank, there were (in 2002), on average, 5.48 exons per gene. (wikipedia.org)
  • 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)
  • Exon shuffling is a molecular mechanism for the formation of new genes. (wikipedia.org)
  • Next generation" sequencing techniques allow for more detailed analysis of exons and introns in multiple genes at the same time. (springer.com)
  • To functionally test these a lot can be achieved with a limited set of protocols, while for the intentional induction of exon skipping different tools and target genes are involved and the translational path from in vitro splicing to in vivo tests in animal models requiring a more extensive set of protocols. (springer.com)
  • Moreover, phenotypes seen in genetic knockout animals may be the result of not only the lack of expression of the deleted gene but also alterations in the expression of genes that are regulated by enhancers in the deleted exons. (sciencemag.org)
  • It has been demonstrated in the past that identification of the period-3 regions helps in predicting the gene locations, and in fact allows the prediction of specific exons within the genes of eucaryotic cells. (psu.edu)
  • In higher organisms, most genes consist of several disconnected regions (exons), which are combined in various ways to produce several different gene transcripts from the same gene. (pnas.org)
  • We identified a core set of 3,800 exons from 1,643 genes that show conservation of strongly tissue-dependent usage patterns from human at least to macaque. (pnas.org)
  • Alternative exon usage has been observed to affect most multiexon genes in mammals ( 1 ⇓ - 3 ). (pnas.org)
  • In short in eukaryotic genes, during mRNA synthesis not all exons are going to the final mRNA, but a selection of them. (biology-online.org)
  • On the basis of this result, the authors went on to use publicly available gene expression and population sequencing data to identify a total of 3955 "brain-critical" exons from 1744 genes that are highly expressed in brain and have a low mutation burden in control individuals but do not show the same pattern in other tissues. (sciencemag.org)
  • They found an enrichment of brain-critical exons in genes associated with ASD risk, genes encoding fragile-X mental retardation protein targets, and genes encoding components of the postsynaptic proteome. (sciencemag.org)
  • Notably, the associations were stronger for specific exons than for whole genes, which may be related to brain-specific isoforms. (sciencemag.org)
  • Genes contain exons which are regions coding for proteins and which are interrupted by the unused sequences called introns . (biology-online.org)
  • Our data demonstrates that splicing error frequencies are not altered by age in peripheral blood cells or in vitro aged fibroblasts in the tested exons of the four investigated genes, indicating a high importance of correct splicing in these proliferating aged cells. (mdpi.com)
  • It was noted that recombination within introns could help assort exons independently and that repetitive segments in the middle of introns could create hotspots for recombination to shuffle the exonic sequences. (wikipedia.org)
  • I did an inner join on genomic sequences to join the expression data with the exons and sorted them from most expressed to least. (mail-archive.com)
  • Exons can include both sequences that code for amino acids (red) and untranslated sequences (grey). (wikipedia.org)
  • In contrast, exons are the sequences within a gene which do get expressed and translated into protein. (madsci.org)
  • In this paper, we present Exon, a user-friendly solution containing tools for online analysis of DNA sequences through compression based profiles. (springer.com)
  • One of these cDNA sequences has three out of four exons plus additional nucleotide sequence at the 3' end of the cDNA. (biology-online.org)
  • and five other exons encode nonrepeated sequences that are shared only with the EGF precursor. (sciencemag.org)
  • More importantly, the introns are spliced out and the exon sequences are fused to form the mature mRNA. (blogspot.com)
  • Exons have been found to include both sequences coding for amino acids and untranslated sequences. (biology-online.org)
  • The base sequences that appear in eukaryotic DNA and are used to make mRNA for a specific protein are the exons of a gene. (biology-online.org)
  • Exon arrays provide the most comprehensive coverage of the genome, including empirically supported and predicted transcribed sequences, enabling the discovery of previously unidentified novel events. (thermofisher.com)
  • Studies and research have shown that the ability to skip certain exons in dystrophin pre-mRNA could circumvent these dystrophin gene errors and provide a potential treatment for DMD patients. (scienceblog.com)
  • This first generation PMO drug candidate is designed to skip exon 51 of the dystrophin gene, allowing for restoration of the reading frame in the dystrophin mRNA sequence. (scienceblog.com)
  • 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)
  • 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)
  • A gff3 file contains features of gene, mRNA, exon and CDS. (mail-archive.com)
  • Exons in a messenger RNA precursor (pre-mRNA). (wikipedia.org)
  • Introns - those parts of the pre-mRNA that are not in the mRNA - (blue) are removed, and the exons are joined together (spliced) to form the final functional mRNA. (wikipedia.org)
  • The second exon is transcriptionally expressed in most species, yet human mRNA reflects only exon 1 and exon 3, suggesting to earlier workers that the gene had a different structure. (mad-cow.org)
  • The question then arises, is human exon 2 cryptic [present but spliced out of mRNA] or is it only expressed in certain rare cell types or tissues or stages of development or at undetectable levels? (mad-cow.org)
  • Hamsters were also once thought to have no exon 2, much less expression, but later it emerged that splice type 1-3 swamped 1-2-3 mRNA unless astrocytes expressing it were present at high levels. (mad-cow.org)
  • Alternatively, exon 2 could have a cryptic function without appearing in mature mRNA. (mad-cow.org)
  • The most common type of alternative splicing events in mammals results in cassette exons, where each such exon can be either included or excluded from the mature mRNA. (igi-global.com)
  • Note that all the coding regions in the exons (hatched) are contiguous in the mature mRNA. (blogspot.com)
  • The introns are removed and the exons are joined together to form the final functional mRNA . (biology-online.org)
  • ASOs were designed to target exon 11 to shift the ratio of lamin A-encoding mRNA to lamin C-encoding mRNA. (jci.org)
  • Thus, our primary findings are that CD33 is a microglial mRNA and that rs3865444 is a proxy SNP for rs12459419 that modulates CD33 exon 2 splicing. (jneurosci.org)
  • In-frame nonsense codons located at a minimum distance upstream of the last exon-exon junction are recognized as premature termination codons (PTCs), targeting the mRNA for degradation. (nature.com)
  • The paper "Prevention of Dystrophic Pathology in Severely Affected Dystrophin/Utrophin-deficient Mice by Morpholino-oligomer-mediated Exon-skipping" details the successful exon skipping and treatment of utrophin/dystrophin double knockout (dKO) mice with a cell-penetrating peptide-conjugated phosphorodiamidate morpholino oligomers (PPMO) targeting exon 23 in dystrophin pre-mRNA. (scienceblog.com)
  • Skipping of exon 23 restored the reading frame of dystrophin mRNA and led to widespread continued translation of dystrophin protein. (scienceblog.com)
  • Exon skipping aims to convert out-of-frame mRNA to in-frame mRNA and induce the production of internally-deleted dystrophin as seen in the less severe Becker muscular dystrophy. (mdpi.com)
  • Disruption of the splicing enhancer sequence within exon 27 of the dystrophin gene by a nonsense mutation induces partial skipping of the exon and is responsible for Becker muscular dystrophy. (nature.com)
  • Oxford, United Kingdom & Bothell, WA, USA - October 20, 2009 - An exon skipping PPMO has demonstrated dramatic effects in the prevention and treatment of severely affected, dystrophin and utrophin-deficient mice, preventing severe deterioration of the treated animals and extending their lifespan. (scienceblog.com)
  • Antisense-mediated exon-skipping represents one of the most promising approaches for the treatment of DMD because of its capacity to correct the reading frame and restore dystrophin expression," said Steve Wilton, Ph.D. Professor at the Center for Neuromuscular and Neurological Disorders, University of Western Australia, Perth, Western Australia, Australia and co-author of the study. (scienceblog.com)
  • Exon skipping and dystrophin restoration was observed for each patient in muscle biopsies taken 4 weeks after the injection. (springer.com)
  • Single cell multiplex PCR amplification of five dystrophin gene exons combined with gender determination. (biomedsearch.com)
  • Another consideration is that only one muscle in the arm or shoulder was examined for dystrophin production and it isn't known if all of the muscles of the body will respond as well to exon skipping treatment. (mda.org.au)
  • Importantly, this review highlights the potential of multiple exon skipping for enabling the production of functionally-corrected dystrophin and for treating symptomatic patients not only with out-of-frame deletions but also those with in-frame deletions. (mdpi.com)
  • We have developed a tool for detecting single exon copy-number variations (CNVs) in targeted next-generation sequencing data: CoNVaDING (Copy Number Variation Detection In Next-generation sequencing Gene panels). (nih.gov)
  • UB2 has a single exon coding for 123 amino acids matching the cDNA. (biology-online.org)
  • This tool comprehensively detects single-exon deletions and duplications in a cost-effective manner and can be used to complement NGS mutation analysis with its reliable exon-level CNV detection. (mysanantonio.com)
  • Neuronal Signaling through Alternative Splicing: Some Exons CaRRE. (sciencemag.org)
  • Alternative splicing (AS) combines different transcript splice junctions that result in transcripts with shuffled exons, alternative 5 or 3 splicing sites, retained introns and different transcript termini. (futura-sciences.com)
  • Alternative splicing, resulting in exon 123 or exon 13 splice products, has been demonstrated for hamster, mouse, rat, cow, and sheep -- in all species studied except human, which so far only shows exon 13 splicing. (mad-cow.org)
  • In our research, we have used Affymetrix Exon Arrays to detect variation in alternative splicing, initiation of transcription, and polyadenylation among humans. (igi-global.com)
  • With approximately four probes per exon and roughly 40 probes per gene, the GeneChip™ Mouse Exon 1.0 ST Array enables two complementary levels of analysis-gene expression and alternative splicing. (thermofisher.com)
  • By analyzing NAS in BRCA1 , we show here that inappropriate exon skipping can be reproduced in vitro , and results from disruption of a splicing enhancer in the coding sequence. (nature.com)
  • Exon shuffling was first introduced in 1978 when Walter Gilbert discovered that the existence of introns could play a major role in the evolution of proteins. (wikipedia.org)
  • Therefore, exon shuffling became a major role in the construction of younger proteins. (wikipedia.org)
  • Moreover, to define more precisely the time when exon shuffling became significant in eukaryotes, the evolutionary distribution of modular proteins that evolved through this mechanism were examined in different organisms (i.e. (wikipedia.org)
  • The LDL receptor appears to be a mosaic protein built up of exons shared with different proteins, and it therefore belongs to several supergene families. (sciencemag.org)
  • Using CD44-Rg fusion proteins we show that the variably spliced exons in CD44E, V8-V10, specifically reduce the lectin function of CD44, while replacement of V8-V10 by an ICAM-1 immunoglobulin domain restores binding to a level comparable to that of CD44H. (rupress.org)
  • Here, we use our study to illustrate the use of Exon Arrays to detect alternative isoforms, to outline the analysis involved, and to point out potential problems that may be encountered by researchers using this technology. (igi-global.com)
  • Analysis of CD33 isoforms identified a common isoform lacking exon 2 ( D2-CD33 ). (jneurosci.org)
  • Multiple probes per exon enable "exon-level" analysis and allow you to distinguish between different isoforms of a gene. (thermofisher.com)
  • Exon skipping uses antisense oligonucleotides (ASOs) to alter transcript splicing for the purpose of rescuing or modulating protein expression. (jci.org)
  • Current exon-level arrays and NGS techniques for CNV detection are plagued with a high number of false-positive calls and are challenging from a cost perspective when verifying numerous exon aberrations with orthogonal methods. (mysanantonio.com)
  • Alternative Isoform Detection Using Exon Arrays. (igi-global.com)
  • bioconductor at r-project.org Oggetto: Re: [BioC] Probe-level analysis of exon arrays using xps Dear Giovanni, In principle you could do the background and normalization steps separately, e.g. (ethz.ch)
  • As you guys know, there is a growing evidence showing that a probe-level analysis (as opposed to a probeset-level or a gene-level analysis) could be useful in analyzing Exon arrays. (ethz.ch)
  • However, using human exon 123 as probe (or subsets thereof), nothing is found in these databases, though mouse exon 123 and mouse exon 13 yield solid returns. (mad-cow.org)
  • The Agilent SurePrint G3 Mouse Exon Microarrays include probes targeting individual exons, making it possible to look beyond the gene to more subtle but relevant expression changes at the exon level. (agilent.com)
  • The goal of this early research is to work toward developing a medicine for people with Duchenne muscular dystrophy amenable to exon 53 skipping. (parentprojectmd.org)
  • It has the potential to treat around 13 percent of boys with Duchenne muscular dystrophy - those with a mutation in the vicinity of exon 51. (mda.org.au)
  • Antisense oligonucleotide-mediated exon skipping is a promising therapy for DMD. (mdpi.com)
  • We will also discuss prospects and challenges in multiple exon skipping therapy, referring to recent progress in antisense chemistry and design, as well as disease models. (mdpi.com)
  • Alternative usage of exons provides genomes with plasticity to produce different transcripts from the same gene, modulating the function, localization, and life cycle of gene products. (pnas.org)
  • The second level is "gene-level" expression analysis, in which multiple probes on different exons are summarized into an expression value of all transcripts from the same gene. (thermofisher.com)
  • In this paper we concentrate on short initial exons and present a method to improve the detection of these short coding regions. (springer.com)
  • Further, the WAM-CpG island approach can be employed to complement existing gene prediction packages to produce substantial improvements in the correct detection of short initial exons. (springer.com)
  • Since this QC shows exactly which exons can be reliably analyzed and which exons are in need of an alternative analysis method, CoNVaDING is not only useful for CNV detection in a research setting, but also in clinical diagnostics. (nih.gov)
  • Researchers at Children's National Medical Center and Greenwood Genetic Center utilize a new, research tool for exon-level CNV detection, the Applied Biosystems™ CytoScan™ XON Suite. (mysanantonio.com)
  • The test, a double nested multiplex polymerase chain reaction assay for the amplification of exons 8, 19, 45, 47 and 51 allows the detection of over 70% of all DMD deletions. (biomedsearch.com)
  • Authoritative and practical Exon Skipping: Methods and Protocols seeks to aid scientists in the continuing study of exon skipping. (springer.com)
  • The theory that exons are basic module s of protein structure that can be shuffled by evolution (much like artificial methods ). (everything2.com)
  • Absence of an exon-encoded enhancer, however, did have functional consequences. (sciencemag.org)
  • In the literature, a considerable number of examples exist of functional diversity created by the alternative usage of exons (reviewed in ref. 7 ). (pnas.org)
  • This gene is more than 45 kilobases in length and contains 18 exons, most of which correlate with functional domains previously defined at the protein level. (sciencemag.org)
  • Because rs3865444 is in the CD33 promoter region, we sought the functional polymorphism by sequencing CD33 from the promoter through exon 4. (jneurosci.org)
  • Minigene RNA splicing studies in BV2 microglial cells established that rs12459419 is a functional single nucleotide polymorphism (SNP) that modulates exon 2 splicing efficiency. (jneurosci.org)
  • a) While some cryptic exons are common between cell types, many cryptic exons are unique to neurons (58), muscle (79) and stem cells [22]. (eurekalert.org)
  • Of the common cryptic exons, several. (eurekalert.org)
  • The Korea Brain Research Institute (President Kyung-jin Kim) announced on Wednesday February 8, 2017 that an international collaborative research team including Senior Researcher Yun Ha Jeong succeeded in discovering a phenomenon that cryptic exons that are related to Lou Gehrig's Disease and Frontotemporal Dementia (FTD) are highly variable depending on the cell types. (eurekalert.org)
  • Scientists expect to elucidate pathogenic mechanisms of Frontotemporal Dementia (FTD) and other diseases once they find how Tdp-43 protein and cryptic exons* interact with each other depending on the cellular context. (eurekalert.org)
  • Cryptic exons are regions of the genome that are normally skipped by the spliceosome due to the presence of adjacent UG microsatellite repeats, the consensus binding site of Tdp-43. (eurekalert.org)
  • The collaborative research team confirmed that different kinds of cryptic exons were produced depending on the cell types such as muscle cells and neurons after an experiment using gene-manipulated mice that were prevented from expressing Tdp-43 protein in the desired cells. (eurekalert.org)
  • Senior Researcher Yun Ha Jeong from the Korea Brain Research Institute said, "This study suggests that Tdp-43 proteinopathy and specific cryptic exons are involved in the process of degenerative brain and muscle disorders in a unique way. (eurekalert.org)
  • Tdp-43 Cryptic Exons are Highly Variable between Cell Types," Molecular Neurodegeneration 2017. (eurekalert.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)
  • Hi folks, I'm trying to find over the entire human genome, for each gene, which exons are the most constitutively expressed. (mail-archive.com)
  • These changes affect some of the transcript cluster and exon cluster IDs. (affymetrix.com)
  • Corrected: There were some cases where the first exon of a transcript was incorrectly treated as a separate transcript. (affymetrix.com)
  • This field is set with the transcript_cluster_id, not exon level probe set id. (affymetrix.com)
  • A single-nucleotide exon has been reported from the Arabidopsis genome. (wikipedia.org)
  • Such alternative exon usage is thought to contribute to the ability of organisms to generate different cell types and tissues from a single genome. (pnas.org)
  • We address this question in a genome-wide manner by analyzing the transcriptomes of five tissues for six primate species, focusing on exons that are 1:1 orthologous in all six species. (pnas.org)
  • Alternative usage of exons is correlated with organismal complexity, and it is thought that by enhancing proteome diversity, it is essential for the ability of a single genome to generate phenotypically diverse tissues ( 9 ). (pnas.org)
  • This exon-level analysis on a whole-genome scale opens the door to detecting specific alterations in exon usage that may play a central role in disease mechanism and etiology. (thermofisher.com)
  • Highest resolution expression analysis, interrogating over 1 million exon clusters within the known and predicted transcribed regions of the entire genome. (thermofisher.com)
  • An exon is any part of a gene that will encode a part of the final mature RNA produced by that gene after introns have been removed by RNA splicing. (wikipedia.org)
  • A similar question arises in exon 1b in sheep -- the splice junction seems unflawed but, unlike in cow, not utilized. (mad-cow.org)
  • To do this, I'd like to combine expression data (RNA-seq or Microarray) and exons data (UCSC track). (mail-archive.com)
  • I've started learning Galaxy and was able to import BED files for UCSC exons (as in the Galaxy 101 tutorial) and a BED file for Affy microarray expression data. (mail-archive.com)
  • The primers and probe are located in exon 1. (abcam.com)
  • 1 About 10 percent of the exon probe sets have fewer than four probes due to the probe selection region length and sequence constraints. (thermofisher.com)
  • In the next step, the spliceosome catalyzes the attack of the -OH group at the end of the 5′ exon on the 3′ splice site. (blogspot.com)
  • There is no correlation between the exons and any protein domains or motifs. (blogspot.com)
  • Figure 1: High-score SR protein motifs in BRCA1 exon 18. (nature.com)
  • The issue is apparently why the donor 3' to exon 1 does not splice with the acceptor 5' of exon 2, which then forces the donor to splice with the acceptor 5' of exon 3 (a region where a polymorphism is found at the polypyrimidine boundary, G-21A ). (mad-cow.org)
  • We identified a single polymorphism that is coinherited with rs3865444, i.e., rs12459419 in exon 2. (jneurosci.org)
  • It turns out that there is also another gene on the complementary strand (gene X). The start codon of the disease gene lines up with the end of the first exon of gene X. Which part of gene X lines up with the mutation? (studentdoctor.net)
  • Gersappe, A. & Pintel, D.J. A premature termination codon interferes with the nuclear function of an exon splicing enhancer in an open reading frame-dependent manner. (nature.com)
  • We propose to rescue exon 20 skipping using an RNA- based approaches that use modified U1 snRNA, named Exon Specific U1snRNA (ExSpeU1), aimed at improving exon definition. (icgeb.org)
  • In vitro splicing of BRCA1 minigene transcripts reproduces the exon-skipping phenotype of a nonsense mutation. (nature.com)
  • Here, we provide an update on DMD genotype-phenotype associations using a global DMD database and further provide the rationale for multiple exon skipping development, particularly for exons 45-55 skipping and an emerging therapeutic concept, exons 3-9 skipping. (mdpi.com)
  • They did not span all the contained exon clusters, PSRs, and probesets. (affymetrix.com)
  • analyzed 25 mouse and human enhancer-associated ChIP-seq data sets in order to identify enhancer peaks that overlap exons and found regulatory transcription factor binding to exonic regions. (sciencemag.org)
  • In fact, in mice, roughly 7% of enhancer peaks overlapped coding exons. (sciencemag.org)
  • Figure 3: Exon skipping correlates with the SF2/ASF enhancer motif score and not with reading frame disruption. (nature.com)
  • A (E139K) PMM2 mutation in carbohydrate-deficient glycoprotein syndrome type Ia disrupting a splicing enhancer resulting in exon 5 skipping. (nature.com)
  • In this webinar, which is sponsored by Thermo Fisher Scientific - Applied Biosystems , participants will learn how a novel exon-level CNV assay can be used to overcome these challenges. (mysanantonio.com)
  • The work supports the exon shuffling theory, which contends that introns act as spacers where breaks for genetic recombination occur. (swarthmore.edu)
  • In other words, the breaks in the chromosomes can be made in the introns, the filler sections, which are marked so as not to be confused with the exons, the sections containing important genetic information. (swarthmore.edu)
  • In parallel, preclinical studies to further optimise treatment regimens are in progress as well as clinical trials for additional exons for exon 44 skipping (PRO044, applicable to 6% of patients). (springer.com)
  • Therefore, if human exon 2 is a molecular fossil without function , this must be a very recent development. (mad-cow.org)
  • Whereas the IKBKAP size and its poorly known regulation complicates replacement gene therapy, the molecular defect renders FD an ideal target for strategies promoting exon 20 inclusion. (icgeb.org)
  • However, a region clearly related to exon 2 was identified in humans from its strong sequence homology to expressed exon 2 in other species. (mad-cow.org)
  • transposon mediated exon shuffling, crossover during sexual recombination of parental genomes and illegitimate recombination . (wikipedia.org)
  • Evolution of eukaryotes is mediated by sexual recombination of parental genomes and since introns are longer than exons most of the crossovers occur in noncoding regions. (wikipedia.org)
  • [1] There are different mechanisms through which exon shuffling occurs: transposon mediated exon shuffling, crossover during sexual recombination of parental genomes and illegitimate recombination. (wikipedia.org)
  • We generated a new mouse model (MMex38) carrying a missense mutation in exon 38 in analogy to a clinically relevant human DYSF variant (DYSF p.Leu1341Pro). (mdc-berlin.de)
  • David Exon was appointed as Consultant Upper GI & General Surgeon in Leicester in 2010. (nuffieldhealth.com)
  • Then, for each gene, I'd like to pick the 1 or 2 exons with the highest levels of expression (my proxy for constitutiveness). (mail-archive.com)
  • For example, let's say a gene has 3 exons and, with the expression data, all 3 exons are equally expressed. (mail-archive.com)
  • That is, how do I get the top 2 exons per gene (highest expressing exons per gene) and, if there are more than 2 with equally high expression, how do I preferentially get the 5` exons? (mail-archive.com)
  • Discover our large selection of Gene Expression & Exon Microarrays. (agilent.com)
  • This includes whole transcriptome gene expression for almost 30 different species, Exon microarrays to analyze splicing variants and gene expression microarrays with comprehensive content, including full LNCipedia databases to provide full coverage of the transcriptome in a single experiment. (agilent.com)
  • Agilent Exon Microarrays are the fast, simple, and cost-effective choice for exon expression analysis, with capabilities to drill down into important RNA changes at the exon level. (agilent.com)
  • LOCUS SPSPEC14 150 bp DNA INV 04-APR-1995 DEFINITION Strongylocentrotus purpuratus Spec1 gene exon 4 (for major calcium-binding protein). (davidson.edu)
  • LOCUS SUSMSP130A 1165 bp DNA INV 15-JUN-1993 DEFINITION S.purpuratus cell surface glycoprotein (msp130) gene, 5' flank and exon 1. (davidson.edu)
  • Speakers will identify research cases that may benefit from an exon-level CNV assay. (mysanantonio.com)