Science: The study of natural phenomena by observation, measurement, and experimentation.Alternative Splicing: A process whereby multiple RNA transcripts are generated from a single gene. Alternative splicing involves the splicing together of other possible sets of EXONS during the processing of some, but not all, transcripts of the gene. Thus a particular exon may be connected to any one of several alternative exons to form a mature RNA. The alternative forms of mature MESSENGER RNA produce PROTEIN ISOFORMS in which one part of the isoforms is common while the other parts are different.NewsEarly Detection of Cancer: Methods to identify and characterize cancer in the early stages of disease and predict tumor behavior.Newspapers: Publications printed and distributed daily, weekly, or at some other regular and usually short interval, containing news, articles of opinion (as editorials and letters), features, advertising, and announcements of current interest. (Webster's 3d ed)Mass Media: Instruments or technological means of communication that reach large numbers of people with a common message: press, radio, television, etc.Neoplasms: New abnormal growth of tissue. Malignant neoplasms show a greater degree of anaplasia and have the properties of invasion and metastasis, compared to benign neoplasms.Prostatic Neoplasms: Tumors or cancer of the PROSTATE.Breast Neoplasms: Tumors or cancer of the human BREAST.Lung Neoplasms: Tumors or cancer of the LUNG.Research Support, U.S. Gov't, Non-P.H.S.Research Support, U.S. Gov't, P.H.S.Research Support, Non-U.S. Gov'tResearch Support, U.S. GovernmentResearch Support, American Recovery and Reinvestment ActResearch Support, N.I.H., ExtramuralResearch Support, N.I.H., IntramuralResearch Support as Topic: Financial support of research activities.PubMed: A bibliographic database that includes MEDLINE as its primary subset. It is produced by the National Center for Biotechnology Information (NCBI), part of the NATIONAL LIBRARY OF MEDICINE. PubMed, which is searchable through NLM's Web site, also includes access to additional citations to selected life sciences journals not in MEDLINE, and links to other resources such as the full-text of articles at participating publishers' Web sites, NCBI's molecular biology databases, and PubMed Central.Cell Differentiation: Progressive restriction of the developmental potential and increasing specialization of function that leads to the formation of specialized cells, tissues, and organs.Molecular Sequence Annotation: The addition of descriptive information about the function or structure of a molecular sequence to its MOLECULAR SEQUENCE DATA record.PaintingsGenomics: The systematic study of the complete DNA sequences (GENOME) of organisms.Software: Sequential operating programs and data which instruct the functioning of a digital computer.Chromosome Mapping: Any method used for determining the location of and relative distances between genes on a chromosome.Turner Syndrome: A syndrome of defective gonadal development in phenotypic females associated with the karyotype 45,X (or 45,XO). Patients generally are of short stature with undifferentiated GONADS (streak gonads), SEXUAL INFANTILISM, HYPOGONADISM, webbing of the neck, cubitus valgus, elevated GONADOTROPINS, decreased ESTRADIOL level in blood, and CONGENITAL HEART DEFECTS. NOONAN SYNDROME (also called Pseudo-Turner Syndrome and Male Turner Syndrome) resembles this disorder; however, it occurs in males and females with a normal karyotype and is inherited as an autosomal dominant.Compound Eye, Arthropod: Light sensory organ in ARTHROPODS consisting of a large number of ommatidia, each functioning as an independent photoreceptor unit.Expressed Sequence Tags: Partial cDNA (DNA, COMPLEMENTARY) sequences that are unique to the cDNAs from which they were derived.Databases, Genetic: Databases devoted to knowledge about specific genes and gene products.Exons: 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.Calcium: A basic element found in nearly all organized tissues. It is a member of the alkaline earth family of metals with the atomic symbol Ca, atomic number 20, and atomic weight 40. Calcium is the most abundant mineral in the body and combines with phosphorus to form calcium phosphate in the bones and teeth. It is essential for the normal functioning of nerves and muscles and plays a role in blood coagulation (as factor IV) and in many enzymatic processes.Signal Transduction: The intracellular transfer of information (biological activation/inhibition) through a signal pathway. In each signal transduction system, an activation/inhibition signal from a biologically active molecule (hormone, neurotransmitter) is mediated via the coupling of a receptor/enzyme to a second messenger system or to an ion channel. Signal transduction plays an important role in activating cellular functions, cell differentiation, and cell proliferation. Examples of signal transduction systems are the GAMMA-AMINOBUTYRIC ACID-postsynaptic receptor-calcium ion channel system, the receptor-mediated T-cell activation pathway, and the receptor-mediated activation of phospholipases. Those coupled to membrane depolarization or intracellular release of calcium include the receptor-mediated activation of cytotoxic functions in granulocytes and the synaptic potentiation of protein kinase activation. Some signal transduction pathways may be part of larger signal transduction pathways; for example, protein kinase activation is part of the platelet activation signal pathway.Elevators and Escalators: Mechanical ascending and descending devices which convey objects and/or people.Molecular Sequence Data: Descriptions of specific amino acid, carbohydrate, or nucleotide sequences which have appeared in the published literature and/or are deposited in and maintained by databanks such as GENBANK, European Molecular Biology Laboratory (EMBL), National Biomedical Research Foundation (NBRF), or other sequence repositories.Base Sequence: The sequence of PURINES and PYRIMIDINES in nucleic acids and polynucleotides. It is also called nucleotide sequence.Neurosciences: The scientific disciplines concerned with the embryology, anatomy, physiology, biochemistry, pharmacology, etc., of the nervous system.RNA, Messenger: RNA sequences that serve as templates for protein synthesis. Bacterial mRNAs are generally primary transcripts in that they do not require post-transcriptional processing. Eukaryotic mRNA is synthesized in the nucleus and must be exported to the cytoplasm for translation. Most eukaryotic mRNAs have a sequence of polyadenylic acid at the 3' end, referred to as the poly(A) tail. The function of this tail is not known for certain, but it may play a role in the export of mature mRNA from the nucleus as well as in helping stabilize some mRNA molecules by retarding their degradation in the cytoplasm.Memory: Complex mental function having four distinct phases: (1) memorizing or learning, (2) retention, (3) recall, and (4) recognition. Clinically, it is usually subdivided into immediate, recent, and remote memory.Amino Acid Sequence: 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.Advanced Oxidation Protein Products: A class of dityrosine-containing protein-derived molecules formed by OXIDATIVE STRESS. Their accumulation in plasma is associated with certain pathological conditions.Protein Biosynthesis: The biosynthesis of PEPTIDES and PROTEINS on RIBOSOMES, directed by MESSENGER RNA, via TRANSFER RNA that is charged with standard proteinogenic AMINO ACIDS.Cloning, Molecular: 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.Proteins: Linear POLYPEPTIDES that are synthesized on RIBOSOMES and may be further modified, crosslinked, cleaved, or assembled into complex proteins with several subunits. The specific sequence of AMINO ACIDS determines the shape the polypeptide will take, during PROTEIN FOLDING, and the function of the protein.Allergy and Immunology: A medical specialty concerned with the hypersensitivity of the individual to foreign substances and protection from the resultant infection or disorder.Bence Jones Protein: An abnormal protein with unusual thermosolubility characteristics that is found in the urine of patients with MULTIPLE MYELOMA.Stress, Physiological: The unfavorable effect of environmental factors (stressors) on the physiological functions of an organism. Prolonged unresolved physiological stress can affect HOMEOSTASIS of the organism, and may lead to damaging or pathological conditions.Periodicals as Topic: A publication issued at stated, more or less regular, intervals.Advertising as Topic: The act or practice of calling public attention to a product, service, need, etc., especially by paid announcements in newspapers, magazines, on radio, or on television. (Random House Unabridged Dictionary, 2d ed)Pinch Strength: Force exerted when using the index finger and the thumb. It is a test for determining maximum voluntary contraction force.Hospital Rapid Response Team: Multidisciplinary team most frequently consisting of INTENSIVE CARE UNIT trained personnel who are available 24 hours per day, 7 days per week for evaluation of patients who develop signs or symptoms of severe clinical deterioration.Gene Expression Regulation, Bacterial: Any of the processes by which cytoplasmic or intercellular factors influence the differential control of gene action in bacteria.Pituitary-Adrenal System: The interactions between the anterior pituitary and adrenal glands, in which corticotropin (ACTH) stimulates the adrenal cortex and adrenal cortical hormones suppress the production of corticotropin by the anterior pituitary.Hypothalamo-Hypophyseal System: A collection of NEURONS, tracts of NERVE FIBERS, endocrine tissue, and blood vessels in the HYPOTHALAMUS and the PITUITARY GLAND. This hypothalamo-hypophyseal portal circulation provides the mechanism for hypothalamic neuroendocrine (HYPOTHALAMIC HORMONES) regulation of pituitary function and the release of various PITUITARY HORMONES into the systemic circulation to maintain HOMEOSTASIS.Interleukins: Soluble factors which stimulate growth-related activities of leukocytes as well as other cell types. They enhance cell proliferation and differentiation, DNA synthesis, secretion of other biologically active molecules and responses to immune and inflammatory stimuli.Cytokines: Non-antibody proteins secreted by inflammatory leukocytes and some non-leukocytic cells, that act as intercellular mediators. They differ from classical hormones in that they are produced by a number of tissue or cell types rather than by specialized glands. They generally act locally in a paracrine or autocrine rather than endocrine manner.Dissertations, Academic as Topic: Dissertations embodying results of original research and especially substantiating a specific view, e.g., substantial papers written by candidates for an academic degree under the individual direction of a professor or papers written by undergraduates desirous of achieving honors or distinction.Inflammation: A pathological process characterized by injury or destruction of tissues caused by a variety of cytologic and chemical reactions. It is usually manifested by typical signs of pain, heat, redness, swelling, and loss of function.Interleukin-6: A cytokine that stimulates the growth and differentiation of B-LYMPHOCYTES and is also a growth factor for HYBRIDOMAS and plasmacytomas. It is produced by many different cells including T-LYMPHOCYTES; MONOCYTES; and FIBROBLASTS.Sepia: A genus of cuttlefish in the family Sepiidae. They live in tropical, subtropical and temperate waters in most oceans.Vascular Endothelial Growth Factor A: The original member of the family of endothelial cell growth factors referred to as VASCULAR ENDOTHELIAL GROWTH FACTORS. Vascular endothelial growth factor-A was originally isolated from tumor cells and referred to as "tumor angiogenesis factor" and "vascular permeability factor". Although expressed at high levels in certain tumor-derived cells it is produced by a wide variety of cell types. In addition to stimulating vascular growth and vascular permeability it may play a role in stimulating VASODILATION via NITRIC OXIDE-dependent pathways. Alternative splicing of the mRNA for vascular endothelial growth factor A results in several isoforms of the protein being produced.Endometrium: The mucous membrane lining of the uterine cavity that is hormonally responsive during the MENSTRUAL CYCLE and PREGNANCY. The endometrium undergoes cyclic changes that characterize MENSTRUATION. After successful FERTILIZATION, it serves to sustain the developing embryo.Vascular Endothelial Growth Factors: A family of angiogenic proteins that are closely-related to VASCULAR ENDOTHELIAL GROWTH FACTOR A. They play an important role in the growth and differentiation of vascular as well as lymphatic endothelial cells.Protein Isoforms: Different forms of a protein that may be produced from different GENES, or from the same gene by ALTERNATIVE SPLICING.Endothelial Growth Factors: These growth factors are soluble mitogens secreted by a variety of organs. The factors are a mixture of two single chain polypeptides which have affinity to heparin. Their molecular weight are organ and species dependent. They have mitogenic and chemotactic effects and can stimulate endothelial cells to grow and synthesize DNA. The factors are related to both the basic and acidic FIBROBLAST GROWTH FACTORS but have different amino acid sequences.Receptors, Vascular Endothelial Growth Factor: A family of closely related RECEPTOR PROTEIN-TYROSINE KINASES that bind vascular endothelial growth factors. They share a cluster of seven extracellular Ig-like domains which are important for ligand binding. They are highly expressed in vascular endothelial cells and are critical for the physiological and pathological growth, development and maintenance of blood and lymphatic vessels.Lymphokines: Soluble protein factors generated by activated lymphocytes that affect other cells, primarily those involved in cellular immunity.Neovascularization, Pathologic: A pathologic process consisting of the proliferation of blood vessels in abnormal tissues or in abnormal positions.

Characterization of an amphioxus paired box gene, AmphiPax2/5/8: developmental expression patterns in optic support cells, nephridium, thyroid-like structures and pharyngeal gill slits, but not in the midbrain-hindbrain boundary region. (1/9069)

On the basis of developmental gene expression, the vertebrate central nervous system comprises: a forebrain plus anterior midbrain, a midbrain-hindbrain boundary region (MHB) having organizer properties, and a rhombospinal domain. The vertebrate MHB is characterized by position, by organizer properties and by being the early site of action of Wnt1 and engrailed genes, and of genes of the Pax2/5/8 subfamily. Wada and others (Wada, H., Saiga, H., Satoh, N. and Holland, P. W. H. (1998) Development 125, 1113-1122) suggested that ascidian tunicates have a vertebrate-like MHB on the basis of ascidian Pax258 expression there. In another invertebrate chordate, amphioxus, comparable gene expression evidence for a vertebrate-like MHB is lacking. We, therefore, isolated and characterized AmphiPax2/5/8, the sole member of this subfamily in amphioxus. AmphiPax2/5/8 is initially expressed well back in the rhombospinal domain and not where a MHB would be expected. In contrast, most of the other expression domains of AmphiPax2/5/8 correspond to expression domains of vertebrate Pax2, Pax5 and Pax8 in structures that are probably homologous - support cells of the eye, nephridium, thyroid-like structures and pharyngeal gill slits; although AmphiPax2/5/8 is not transcribed in any structures that could be interpreted as homologues of vertebrate otic placodes or otic vesicles. In sum, the developmental expression of AmphiPax2/5/8 indicates that the amphioxus central nervous system lacks a MHB resembling the vertebrate isthmic region. Additional gene expression data for the developing ascidian and amphioxus nervous systems would help determine whether a MHB is a basal chordate character secondarily lost in amphioxus. The alternative is that the MHB is a vertebrate innovation.  (+info)

The role of gene splicing, gene amplification and regulation in mosquito insecticide resistance. (2/9069)

The primary routes of insecticide resistance in all insects are alterations in the insecticide target sites or changes in the rate at which the insecticide is detoxified. Three enzyme systems, glutathione S-transferases, esterases and monooxygenases, are involved in the detoxification of the four major insecticide classes. These enzymes act by rapidly metabolizing the insecticide to non-toxic products, or by rapidly binding and very slowly turning over the insecticide (sequestration). In Culex mosquitoes, the most common organophosphate insecticide resistance mechanism is caused by co-amplification of two esterases. The amplified esterases are differentially regulated, with three times more Est beta 2(1) being produced than Est alpha 2(1). Cis-acting regulatory sequences associated with these esterases are under investigation. All the amplified esterases in different Culex species act through sequestration. The rates at which they bind with insecticides are more rapid than those for their non-amplified counterparts in the insecticide-susceptible insects. In contrast, esterase-based organophosphate resistance in Anopheles is invariably based on changes in substrate specificities and increased turnover rates of a small subset of insecticides. The up-regulation of both glutathione S-transferases and monooxygenases in resistant mosquitoes is due to the effects of a single major gene in each case. The products of these major genes up-regulate a broad range of enzymes. The diversity of glutathione S-transferases produced by Anopheles mosquitoes is increased by the splicing of different 5' ends of genes, with a single 3' end, within one class of this enzyme family. The trans-acting regulatory factors responsible for the up-regulation of both the monooxygenase and glutathione S-transferases still need to be identified, but the recent development of molecular tools for positional cloning in Anopheles gambiae now makes this possible.  (+info)

Expression of the naturally occurring truncated trkB neurotrophin receptor induces outgrowth of filopodia and processes in neuroblastoma cells. (3/9069)

We have investigated the effects of the truncated trkB receptor isoform T1 (trkB.T1) by transient transfection into mouse N2a neuroblastoma cells. We observed that expression of trkB.T1 leads to a striking change in cell morphology characterized by outgrowth of filopodia and processes. A similar morphological response was also observed in SH-SY5Y human neuroblastoma cells and NIH3T3 fibroblasts transfected with trkB.T1. N2a cells lack endogenous expression of trkB isoforms, but express barely detectable amounts of its ligands, brain-derived neurotrophic factor (BDNF) and neurotrophin-4 (NT-4). The morphological change was ligand-independent, since addition of exogenous BDNF or NT-4 or blockade of endogenous trkB ligands did not influence this response. Filopodia and process outgrowth was significantly suppressed when full-length trkB.TK+ was cotransfected together with trkB.T1 and this inhibitory effect was blocked by tyrosine kinase inhibitor K252a. Transfection of trkB.T1 deletion mutants showed that the morphological response is dependent on the extracellular, but not the intracellular domain of the receptor. Our results suggest a novel ligand-independent role for truncated trkB in the regulation of cellular morphology.  (+info)

Differential stability of the DNA-activated protein kinase catalytic subunit mRNA in human glioma cells. (4/9069)

DNA-dependent protein kinase (DNA-PK) functions in double-strand break repair and immunoglobulin [V(D)J] recombination. We previously established a radiation-sensitive human cell line, M059J, derived from a malignant glioma, which lacks the catalytic subunit (DNA-PKcs) of the DNA-PK multiprotein complex. Although previous Northern blot analysis failed to detect the DNA-PKcs transcript in these cells, we show here through quantitative studies that the transcript is present, albeit at greatly reduced (approximately 20x) levels. Sequencing revealed no genetic alteration in either the promoter region, the kinase domain, or the 3' untranslated region of the DNA-PKcs gene to account for the reduced transcript levels. Nuclear run-on transcription assays indicated that the rate of DNA-PKcs transcription in M059J and DNA-PKcs proficient cell lines was similar, but the stability of the DNA-PKcs message in the M059J cell line was drastically (approximately 20x) reduced. Furthermore, M059J cells lack an alternately spliced DNA-PKcs transcript that accounts for a minor (5-20%) proportion of the DNA-PKcs message in all other cell lines tested. Thus, alterations in DNA-PKcs mRNA stability and/or the lack of the alternate mRNA may result in the loss of DNA-PKcs activity. This finding has important implications as DNA-PKcs activity is essential to cells repairing damage induced by radiation or radiomimetric agents.  (+info)

Selection and characterization of pre-mRNA splicing enhancers: identification of novel SR protein-specific enhancer sequences. (5/9069)

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)

Alterations in the conserved SL1 trans-spliced leader of Caenorhabditis elegans demonstrate flexibility in length and sequence requirements in vivo. (6/9069)

Approximately 70% of mRNAs in Caenorhabditis elegans are trans spliced to conserved 21- to 23-nucleotide leader RNAs. While the function of SL1, the major C. elegans trans-spliced leader, is unknown, SL1 RNA, which contains this leader, is essential for embryogenesis. Efforts to characterize in vivo requirements of the SL1 leader sequence have been severely constrained by the essential role of the corresponding DNA sequences in SL1 RNA transcription. We devised a heterologous expression system that circumvents this problem, making it possible to probe the length and sequence requirements of the SL1 leader without interfering with its transcription. We report that expression of SL1 from a U2 snRNA promoter rescues mutants lacking the SL1-encoding genes and that the essential embryonic function of SL1 is retained when approximately one-third of the leader sequence and/or the length of the leader is significantly altered. In contrast, although all mutant SL1 RNAs were well expressed, more severe alterations eliminate this essential embryonic function. The one non-rescuing mutant leader tested was never detected on messages, demonstrating that part of the leader sequence is essential for trans splicing in vivo. Thus, in spite of the high degree of SL1 sequence conservation, its length, primary sequence, and composition are not critical parameters of its essential embryonic function. However, particular nucleotides in the leader are essential for the in vivo function of the SL1 RNA, perhaps for its assembly into a functional snRNP or for the trans-splicing reaction.  (+info)

Mammalian staufen is a double-stranded-RNA- and tubulin-binding protein which localizes to the rough endoplasmic reticulum. (7/9069)

Staufen (Stau) is a double-stranded RNA (dsRNA)-binding protein involved in mRNA transport and localization in Drosophila. To understand the molecular mechanisms of mRNA transport in mammals, we cloned human (hStau) and mouse (mStau) staufen cDNAs. In humans, four transcripts arise by differential splicing of the Stau gene and code for two proteins with different N-terminal extremities. In vitro, hStau and mStau bind dsRNA via each of two full-length dsRNA-binding domains and tubulin via a region similar to the microtubule-binding domain of MAP-1B, suggesting that Stau cross-links cytoskeletal and RNA components. Immunofluorescent double labeling of transfected mammalian cells revealed that Stau is localized to the rough endoplasmic reticulum (RER), implicating this RNA-binding protein in mRNA targeting to the RER, perhaps via a multistep process involving microtubules. These results are the first demonstration of the association of an RNA-binding protein in addition to ribosomal proteins, with the RER, implicating this class of proteins in the transport of RNA to its site of translation.  (+info)

Expression of novel alternatively spliced isoforms of the oct-1 transcription factor. (8/9069)

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)

*Alternative splicing

Research Group dealing with alternative Splicing issues and mis-splicing in human diseases Alternative Splicing of ion channels ... Since then, alternative splicing has been found to be ubiquitous in eukaryotes. The "record-holder" for alternative splicing is ... These databases are useful for finding genes having pre-mRNAs undergoing alternative splicing and alternative splicing events. ... A General Definition and Nomenclature for Alternative Splicing Events at SciVee AStalavista (Alternative Splicing landscape ...

*Alternative splicing annotation project

... (ASAP) is a database for alternative splicing data. The purpose of this project was to ... Lee, C., Atanelov, L., Modrek, B., & Xing, Y. (2003). ASAP: the alternative splicing annotation project. Nucleic Acids Research ... analysis and comparative genomics of alternative splicing in 15 animal species". Nucleic Acids Res. England. 35 (Database issue ... AspicDB RNA splicing Kim, Namshin; Alekseyenko Alexander V; Roy Meenakshi; Lee Christopher (Jan 2007). "The ASAP II database: ...

*Human-transcriptome database for alternative splicing

The Human-transcriptome DataBase for Alternative Splicing (H-DBAS) is a database of alternatively spliced human transcripts ... Alternative splicing Takeda, Jun-ichi; Suzuki Yutaka; Nakao Mitsuteru; Kuroda Tsuyoshi; Sugano Sumio; Gojobori Takashi; ... alternative splicing database of completely sequenced and manually annotated full-length cDNAs based on H-Invitational". ...

*Alternative splicing and transcript diversity database

... polyadenylation and splicing variant data. Alternative splicing annotation project AspicDB RNA splicing Koscielny, Gautier; Le ... The Alternative Splicing and Transcript Diversity database (ASTD) is a database of alternative transcripts containing ... The Alternative Splicing and Transcript Diversity database". Genomics. United States. 93 (3): 213-20. doi:10.1016/j.ygeno. ...

*SARS conspiracy theory

"Gene Splicing Mechanism , Alternative Splicing Tutorial , Splice Variant Detection". www.premierbiosoft.com. Retrieved 2016-05- ... believe is a clear sign of the well understood field of gene splicing. "Sars biological weapon?". www.news24.com. 11 April 2003 ...

*Low-density lipoprotein receptor-related protein 8

Are You reelin in the Years? Not without Alternative Splicing. ... alternative splicing, and transcription units of the human ... ApoER2 splice variants can act as a receptor for alpha-2-macroglobulin which can have a role in clearance of alpha-2- ... In ApoER2, there is a proline-rich 59 amino acid insert encoded by the alternatively spliced exon 19. This insert allows for ... Studies with mice have shown that knocking out ApoER2 or just the alternatively spliced exon 19 causes a much greater ...

*ELK1

Alternative splicing produces ∆Elk1. This variant lacks part of the DNA-binding domain that allows interaction with SRF. On the ... Elk1 also interacts with BRCA1 splice variants, namely BRCA1a and BRCA1b. This interaction enhances BRCA1-mediated growth ... "c-Fos oncogene regulator Elk-1 interacts with BRCA1 splice variants BRCA1a/1b and enhances BRCA1a/1b-mediated growth ...

*HNRNPA1

Evidence for alternative splicing". J. Mol. Biol. 207 (3): 491-503. doi:10.1016/0022-2836(89)90459-2. PMID 2760922. Buvoli M, ... Buvoli M, Cobianchi F, Bestagno MG, Mangiarotti A, Bassi MT, Biamonti G, Riva S (1990). "Alternative splicing in the human gene ... and may modulate splice site selection. Multiple alternatively spliced transcript variants have been found for this gene but ... These variants have multiple alternative transcription initiation sites and multiple polyA sites. Heterogeneous nuclear ...

*Fucosyltransferase 3

Alternative splicing, polyadenylation, and isoforms". The Journal of Biological Chemistry. 270 (34): 20112-22. doi:10.1074/jbc. ... Multiple alternatively spliced variants, encoding the same protein, have been found for this gene. Cluster of differentiation ...

*FUT6

Alternative splicing, polyadenylation, and isoforms". J. Biol. Chem. 270 (34): 20112-22. doi:10.1074/jbc.270.34.20112. PMID ... 2004). "Activity and tissue distribution of splice variants of alpha6-fucosyltransferase in human embryogenesis". Glycobiology ... large-scale identification and characterization of putative alternative promoters of human genes". Genome Res. 16 (1): 55-65. ...

*MBNL1

"Muscleblind proteins regulate alternative splicing". The EMBO Journal. 23 (15): 3103-12. doi:10.1038/sj.emboj.7600300. PMC ... "Colocalization of muscleblind with RNA foci is separable from mis-regulation of alternative splicing in myotonic dystrophy". ... CUG-BP1 and hnRNP H proteins in DM1-associated aberrant IR splicing". The EMBO Journal. 25 (18): 4271-83. doi:10.1038/sj.emboj. ... "MBNL1 is the primary determinant of focus formation and aberrant insulin receptor splicing in DM1". The Journal of Biological ...

*NUDT1

Alternative splicing of transcription products". The Journal of Biological Chemistry. 272 (28): 17843-50. doi:10.1074/jbc. ... Several alternatively spliced transcript variants, some of which encode distinct isoforms, have been identified. Additional ... "Multi-forms of human MTH1 polypeptides produced by alternative translation initiation and single nucleotide polymorphism". ...

*FUT5

Alternative splicing, polyadenylation, and isoforms". J. Biol. Chem. 270 (34): 20112-22. doi:10.1074/jbc.270.34.20112. PMID ...

*Sequence alignment

Kim N; Lee C (2008). "Bioinformatics detection of alternative splicing". Methods Mol. Biol. Methods in Molecular Biology™. 452 ... can be aligned to a sequenced genome to find where there are genes and get information about alternative splicing and RNA ... BLAST was developed to provide a faster alternative to FASTA without sacrificing much accuracy; like FASTA, BLAST uses a word ... but does not indicate how much superior a given alignment is to alternative alignments of the same sequences. Measures of ...

*Aminoacyl tRNA synthetase

Lareau, LF; Green, RE (June 1, 2004). "The evolving roles of alternative splicing". Current Opinion in Structural Biology. 14 ( ...

*IHPK1

Alternative splicing occurs for this gene; however, the full-length nature of all transcript variants has not yet been ...

*GIT2

This gene undergoes extensive alternative splicing; although ten transcript variants have been described, the full length ... Functional diversity of GIT2 through alternative splicing". The Journal of Biological Chemistry. 275 (29): 22373-80. doi: ...

*ECgene

... is a database of genomic annotations taking alternative splicing events into consideration. Alternative splicing TassDB ... genome annotation for alternative splicing". Nucleic Acids Res. England. 33 (Database issue): D75-9. doi:10.1093/nar/gki118. ...

*NXF1

Alternative splicing results in transcript variants. The LRRs and NTF2-like domains are required for export activity. The ... "Multipotent genetic suppression of retrotransposon-induced mutations by Nxf1 through fine-tuning of alternative splicing". PLoS ... is a component of the splicing-dependent exon-exon junction complex". EMBO J. England. 20 (22): 6424-33. doi:10.1093/emboj/ ...

*ADCY6

Alternative splicing generates 2 transcript variants. GRCh38: Ensembl release 89: ENSG00000174233 - Ensembl, May 2017 GRCm38: ...

*PCDH1

Alternative splicing occurs in this gene. GRCh38: Ensembl release 89: ENSG00000156453 - Ensembl, May 2017 GRCm38: Ensembl ...

*Hollywood (database)

Hollywood is a RNA splicing database containing data for the splicing of orthologous genes in different species. Alternative ... a comparative relational database of alternative splicing". Nucleic Acids Res. England. 34 (Database issue): D56-62. doi: ... splicing EDAS AspicDB Holste, Dirk; Huo George; Tung Vivian; Burge Christopher B (Jan 2006). "HOLLYWOOD: ...

*MBNL3

2005). "Muscleblind proteins regulate alternative splicing". EMBO J. 23 (15): 3103-12. doi:10.1038/sj.emboj.7600300. PMC 514918 ...

*MBNL2

2005). "Muscleblind proteins regulate alternative splicing". EMBO J. 23 (15): 3103-12. doi:10.1038/sj.emboj.7600300. PMC 514918 ... Several alternatively spliced transcript variants have been described but the full-length natures of only some have been ...

*Small nucleolar RNA

One such function is the regulation of alternative splicing of the trans gene transcript, which is done by the snoRNA HBII-52, ... For example, it appears that the C/D box snoRNA SNORD115 regulates the alternative splicing of the serotonin 2C receptor mRNA ... Kishore S, Stamm S (January 2006). "The snoRNA HBII-52 regulates alternative splicing of the serotonin receptor 2C". Science. ... Kishore S, Stamm S (2006). "The snoRNA HBII-52 regulates alternative splicing of the serotonin receptor 2C". Science. 311 (5758 ...

*Gammapapillomavirus

DNA-templated transcription, with some alternative splicing mechanism is the method of transcription. The virus exits the host ...
[115 Pages Report] Check for Discount on Global Neutral Alternative Protein Market by Manufacturers, Countries, Type and Application, Forecast to 2022 report by Global Info Research. Alternative proteins, such as plant-based meat substitutes and edible...
Production of mRNA in eukaryotic cells involves not only transcription but also various processing reactions such as splicing. Recent experiments have indicated that there are direct physical connections between components of the transcription and processing machinery, supporting previous suggestions that pre-mRNA splicing occurs co-transcriptionally. Here we have used a novel functional approach to demonstrate co-transcriptional regulation of alternative splicing. Exon 3 of the alpha-tropomyosin gene is specifically repressed in smooth muscle cells. By delaying synthesis of an essential downstream inhibitory element, we show that the decision to splice or repress exon 3 occurs during a limited window of opportunity following transcription, indicating that splice site selection proceeds rapidly after transcription.
How to silence two different alternative splicing sequences - posted in siRNA, microRNA and RNAi: I need to silence 2 different alternative splicing sequences. does anyone knows how can i do it? Thanx Dr. andrew [email protected]
Stein, H. H. 2012. Utilization of co-products from corn and soybeans, and alternative proteins by pigs. Pages 82-90 in Proceedings of the Chinese Swine Industry Symposium, Shanghai, October 24-26, 2012. Link to full text (.pdf). ...
London, 13 February 2018 - As alternative proteins become mainstream, Nestlé and Tesco are named the best declared companies, while Costco has been called out for its inadequate response
SR proteins are required for constitutive pre-mRNA splicing and also regulate alternative splice site selection in a concentration-dependent manner. They have a modular structure that consists of one or two RNA-recognition motifs (RRMs) and a COOH-terminal arginine/serine-rich domain (RS domain). We have analyzed the role of the individual domains of these closely related proteins in cellular distribution, subnuclear localization, and regulation of alternative splicing in vivo. We observed striking differences in the localization signals present in several human SR proteins. In contrast to earlier studies of RS domains in the Drosophila suppressor-of-white-apricot (SWAP) and Transformer (Tra) alternative splicing factors, we found that the RS domain of SF2/ASF is neither necessary nor sufficient for targeting to the nuclear speckles. Although this RS domain is a nuclear localization signal, subnuclear targeting to the speckles requires at least two of the three constituent domains of SF2/ASF, ...
Immune responses must be tightly controlled for dose, location, strength and duration using genetic, epigenetic or biochemical regulation. Among these, the generation of alternatively-spliced transcripts is an efficient and dynamic way to increase transcriptional and proteomic diversity. Specifically, this thesis explains how splice variation dictates the biological functions of interleukin-22 (IL-22) binding protein (IL-22BP) and interferon lambda 4 (IFNλ4), two proteins that participate in key cytokine responses to infection and inflammation. IL-22BP is a soluble receptor for IL-22 that is expressed as three isoforms in humans, IL-22BPi1, IL-22BPi2 and IL-22BPi3. The murine homolog of IL-22BPi2 has been characterized as an antagonist of IL-22 while the physiological relevance of IL-22BPi1 and IL-22BPi3 are unknown. Here, we present findings demonstrating that alternative splicing tailors IL-22BP activity to specific spatiotemporal conditions. Inclusion of a unique third exon renders IL-22BPi1 ...
Susceptibility to prostate or endometrial cancer is linked with obesity, a state of oestrogen excess. Oestrogen receptor (ER) splice variants may be responsible for the tissue-level of ER activity. Such micro-environmental regulation may modulate cancer initiation and/or progression mechanisms. Real-time reverse transcriptase (RT) polymerase chain reaction (PCR) was used to quantitatively assess the levels of four ER splice variants (ERαΔ3, ERαΔ5, ERβ2 and ERβ5), plus the full-length parent isoforms ERα and ERβ1, in high-risk [tumour-adjacent prostate (n = 10) or endometrial cancer (n = 9)] vs. low-risk [benign prostate (n = 12) or endometrium (n = 9)], as well as a comparison of UK (n = 12) vs. Indian (n = 15) benign prostate. All three tissue groups expressed the ER splice variants at similar levels, apart from ERαΔ5. This splice variant was markedly raised in all of the tumour-adjacent prostate samples compared to benign tissues. Immunofluorescence analysis for ERβ2 in prostate tissue
Because this is the first large-scale study relating ribosome loading to transcript structure, the frequency with which these regulated changes in transcript structure occur across nature is unknown. However, the suggestion that 9-18% of mammalian transcripts may have alternative first exons [12] is provocative. Two mammalian genes, in which alternative first exons were found to modify translation, are the gene encoding TIMP (tissue inhibitor of metalloproteinases) and the oncogene mdm2. With both of these genes, the translational efficiencies of the transcripts are regulated by changes in promoter utilization, which lead to altered 5 leaders [36, 37].. In yeast, use of alternative promoters has been shown in some cases to produce different proteins. The SUC2 and KAR4 genes both contain multiple promoters, which generate different protein products with different biologic activities [38, 39]. Similarly, the short forms of the CRH1, KAR5, PRM2, PRP39, PRY3, ASP3, and AQY1 mRNAs identified in this ...
Research Areas: Alternative Splicing, Bioinformatics Biotechnology, Cellular/Molecular Biology, Computational Methods, Next Gen Sequencing, Transriptome. Departments: Computer Science. Primary Investigator: Jinze Liu. ABI: Exon Splice Pattern Characterization of the Vho1e ...
My PhD project focused on the cloning and characterization of mRNA alternative splice variants of the human prostaglandin F2 alpha (FP) receptor. Initially, our hypothesis was based on identification of an ovine FPB but includes any splice variant of the FP receptor. Interestingly, we identified a 6-TM mRNA splice variant designated hFPs. hFPs is the first putative 6-TM prostaglandin receptor splice variant identified in humans and was cloned from human heart and placenta. Methods include utilizing Rapid Amplification of cDNA Ends (RACE) PCR, subcloning, southern and northern blot analysis, and DNA sequencing to obtain FP receptor clones. DNA sequences were analyzed using MacVector computer software. Once FP isoforms were identified, sequences were confirmed using RT-PCR and receptor characterization was determined utilizing radioligand binding assays, functional studies as well as protein chemistry and immunohistochemical labeling of human tissue. Radioligand binding assays were done using cell ...
The full-length oestrogen receptor (ER) exists in most vertebrates as two separately encoded isoforms. ER splice variants represent truncated or otherwise modified versions of the full-length alpha or beta isoforms of the parent receptor. ERalpha is found on chromosome 6q and encodes a 595 amino acid protein, while ERbeta is found on chromosome 14q and encodes a 530 amino acid protein. These receptors possess differing ligand affinities, are differentially expressed in a tissue-specific fashion and may act antagonistically. Their altered expression has been implicated in the pathophysiology of a diverse range of conditions from cancer progression in hormone-responsive tissues to neurodegenerative disease. Variously co-expressed with full-length ERs, ER splice variants may have a positive or negative influence on transcription either by modifying the effect of the parent receptor or through their own intrinsic activity. To date, the vast majority of studies have used generic primers or antibodies against
Iain F Davidson, Daniela Goetz, Maciej P Zaczek, Maxim I Molodtsov, Pim J Huis in t Veld, Florian Weissmann, Gabriele Litos, David A Cisneros, Maria Ocampo‐Hafalla, Rene Ladurner, Frank Uhlmann, Alipasha Vaziri, Jan‐Michael Peters ...
We start with a feature of type "gene" with the ID "EDEN". This has three alternative splice forms named EDEN.1, EDEN.2 and EDEN.3. To tell GBrowse that each of these splice forms are part of the same gene, we give each one a Parent attribute of "EDEN" corresponding to the ID of the parent gene. Now consider mRNA EDEN.1. It has a five_prime_UTR feature, a three_prime_UTR feature, and four CDS features. To indicate that the CDS and UTR features belong to the mRNA, we give the mRNA a unique ID of "EDEN.1" and give each of the subfeatures a corresponding parent. This pattern repeats for each of the other two splice forms. Note how the five_prime_UTR of EDEN.3 is split in two parts. We use "Name" to give the gene and its alternative splice forms a human-readable name, and use Note to provide a description for the gene as a whole (you can add notes to the individual mRNAs but they wont display by default). The Index=1 attribute is a hint to some indexed database to make the mRNAs searchable by name. ...
OpenHelix provides on-line and onsite training on bioinformatics and genomics resources. OpenHelix encourages faster and more effective research by enabling the efficient use of publicly available tools to access biological data. OpenHelix tutorial suites on publicly available biomedical resources include an online narrated tutorial as well as PowerPoint slides, handouts and exercises. Customers can effectively and efficiently learn to use a resource and save time and money when teaching others by using the downloadable materials.
OpenHelix provides on-line and onsite training on bioinformatics and genomics resources. OpenHelix encourages faster and more effective research by enabling the efficient use of publicly available tools to access biological data. OpenHelix tutorial suites on publicly available biomedical resources include an online narrated tutorial as well as PowerPoint slides, handouts and exercises. Customers can effectively and efficiently learn to use a resource and save time and money when teaching others by using the downloadable materials.
Recent data show the IL32 gene has at least nine transcript variants. The aim of this current study is to characterize the different transcript variants based on the latest sequencing data deposited in the National Center for Biotechnology Information (NCBI) and determine which variants are responsible for the differential pattern of gene expression previously observed in MCF7 compared to MDA MB231 cell lines. Analyses of the nine transcript variants showed their sequences were incredibly similar. Other than variant 9, all of the variants differed from variant 1 by deletions. PCR analyses showed that the longer transcript variants contributed more to differential gene expression observed in the MDA MB231 compared to MCF7 cell lines. Because of the similarities between the variant sequences, when determining differential expression in the breast cell lines, investigators should consider strategies that target analyses of a combination of the longer IL32 transcript variants.
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By Katia Merten-Lentz, partner at Keller and Heckman, and Oliver Hartmanm, legal consultant at Keller and Heckman Pressure is rising for the development of a legal definition of vegan and vegetarian food in Europe but national governments are moving ahead of the European Commission in this regard. ...
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The number of clusters with alternative splicing increases with the number of ESTs per cluster as shown in Figure 1, but attains a maximum between 50-300 ESTs per cluster. Approximately one-third (30%) of the clusters with 50-300 ESTs contain alternative splice variants. This estimate is based on the assumption that the number of ESTs and hence the coverage of the individual gene is more important than expression level when the aim is to identify alternative splicing. A decrease is observed in clusters with more than 300 ESTs, most likely explained by the low number of clusters in this category. The results indicate that a cluster size of at least 50 ESTs is optimal for detection of alternative splicing. The estimated 30% porcine genes with alternative splicing are in agreement with large-scale estimations of alternative splicing data based on EST predictions in human and mouse. Human EST comparisons showed that 35% [5] and 38% [1] of the human genes had alternative splicing and in mouse the ...
A typical fully processed mRNA includes one reference-protein coding ORF (RefORF) or coding sequence. This overly simplistic view is however challenged by recent evidence of translation of alternative ORFs (AltORFs). AltORFs are defined as ORFs occurring either in untranslated regions, or overlapping the RefORF in the non-canonical +2 and +3 reading frames. The use of alternative translation initiation is well-described for viruses and provide small viral genomes with an increased coding capacity, but has been overlooked in eukaryotes. To address this issue, we generated a database of predicted AltORFs in the human transcriptome. We identified 83,886 AltORFs with a minimum size of 40 codons. This threshold was established to increase the chances of detecting the predicted alternative proteins by proteomic techniques, including tryptic digestion and mass spectrometry, and SDS-PAGE. For the majority of mRNAs (87.58 %) we found at least one predicted AltORF and, on average, 3.88 predicted AltORFs ...
I recently had a chance to talk science with my old friend and colleague Jack Greenblatt. He has recently teamed up with some of my other colleagues at the University of Toronto to publish a paper on alternative splicing in mouse cells. Over the years I have had numerous discussions with these colleagues since they are proponents of massive alternative splicing in mammals. I think most splice variants are due to splicing errors.. Theres always a problem with terminology whenever we get involved in this debate. My position is that its easy to detect splice variants but they should be called "splice variants" until it has been firmly established that the variants have a biological function. This is not a distinction thats acceptable to proponents of massive alternative splicing. They use the term "alternative splicing" to refer to any set of processing variants regardless of whether they are splicing errors or real examples of regulation. This sometimes makes it difficult to have a discussion ...
As noted above, many groups have documented abnormal or alternative mRNA splicing in cancer cells. An increasing body of evidence suggests that in several cases the novel protein that is produced by the new mRNA alters the characteristics of the expressing cancer cell. Here, we will focus on five examples: DNMT3B, BRCA1, KLF6, Ron, Gemin5, chosen to highlight specific features of aberrant splicing in cancer cells.. DNA methylation is catalyzed by three enzymes in human cells: DNMT1, DNMT3A and DNMT3B, and cancer cells are characterized by abnormal splicing of the DNMT3B gene. There are several splice forms found in non-transformed cells: DNMT3B1 (which contains all of the protein encoding exons 2-23); DNMT3B2 (which lacks exon 10); DNMT3B3 (which lacks exons 10, 21 and 22); and DNMT3B6 (which is expressed from a different promoter that adds 12 amino acids to the N-terminus of the protein). Several aberrant DNMT3B transcripts have been found in cancer cell lines and primary tumors that produce ...
Alternative splicing is pervasive among complex eukaryote species. For some genes shared by numerous species, dozens of alternative transcripts are already annotated in databases. Most recent studies
Cette s lection propose, par institution dappartenance des coauteurs, la liste des publications cosign es par le Cirad et ses partenaires depuis 2008 : articles de revues, ouvrages et chapitres douvrages, actes de congr s, th ses et m moires HDR r f renc s dans la base de donn es documentaires du Cirad, Agritrop. Un acc s au texte int gral est propos lorsquil est disponible. ...
p,Transcript Support Level 1, when transcripts are supported by at least one non-suspect mRNA.,/p,,p,The ,a href=https://genome.ucsc.edu/cgi-bin/hgc?hgsid=423831555_sqRhAapgi8atmzzBPBAz8Me5797J&c=chr14&o=94517268&t=94547548&g=wgEncodeGencodeCompV19&i=ENST00000544005.1#tsl target=_self,Transcript Support Level,/a, (TSL) is a method to highlight the well-supported and poorly-supported transcript models for users. The method relies on the primary data that can support full-length transcript structure: mRNA and EST alignments supplied by UCSC and Ensembl.,/p,TSL:1The GENCODE set is the gene set for human and mouse. ,a href=/Help/Glossary?id=500 class=popup,GENCODE Basic,/a, is a subset of representative transcripts (splice variants).GENCODE basic,p,ALTERNATIVE2 - APPRIS candidate principal isoform that appears to be conserved in fewer than three tested non-primate species.,/p,,p,,a class=popup href=/Homo_sapiens/Help/Glossary?id=521,APPRIS,/a, is a system to annotate alternatively ...
p,Transcript Support Level 1, when transcripts are supported by at least one non-suspect mRNA.,/p,,p,The ,a href=https://genome.ucsc.edu/cgi-bin/hgc?hgsid=423831555_sqRhAapgi8atmzzBPBAz8Me5797J&c=chr14&o=94517268&t=94547548&g=wgEncodeGencodeCompV19&i=ENST00000544005.1#tsl target=_self,Transcript Support Level,/a, (TSL) is a method to highlight the well-supported and poorly-supported transcript models for users. The method relies on the primary data that can support full-length transcript structure: mRNA and EST alignments supplied by UCSC and Ensembl.,/p,TSL:1The GENCODE set is the gene set for human and mouse. ,a href=/Help/Glossary?id=500 class=popup,GENCODE Basic,/a, is a subset of representative transcripts (splice variants).GENCODE basic,p,PRINCIPAL1 - APPRIS candidate principal isoform.,/p,,p,,a class=popup href=/Homo_sapiens/Help/Glossary?id=521,APPRIS,/a, is a system to annotate alternatively spliced transcripts based on a range of computational methods.,/p,APPRIS P1 ...
p,Transcript Support Level 1, when transcripts are supported by at least one non-suspect mRNA.,/p,,p,The ,a href=https://genome.ucsc.edu/cgi-bin/hgc?hgsid=423831555_sqRhAapgi8atmzzBPBAz8Me5797J&c=chr14&o=94517268&t=94547548&g=wgEncodeGencodeCompV19&i=ENST00000544005.1#tsl target=_self,Transcript Support Level,/a, (TSL) is a method to highlight the well-supported and poorly-supported transcript models for users. The method relies on the primary data that can support full-length transcript structure: mRNA and EST alignments supplied by UCSC and Ensembl.,/p,TSL:1The GENCODE set is the gene set for human and mouse. ,a href=/Help/Glossary?id=500 class=popup,GENCODE Basic,/a, is a subset of representative transcripts (splice variants).GENCODE basic ...
Detection of BORIS expression from different alternative promoters and stability of BORIS alternative transcripts. (A) Unique BORIS cDNA sequences attached to p
These little variations endogenous LRTs cause, in protein structure or protein expression, could be a huge driving force behind speciation and diversity! (microRNAs have a role in this too!). Well, weve got a minor problem trying to address the impact of LTRs on gene expression in humans. We do, like, these huge data mining experiments which tell us "OMG LIEK THEIR ALL ACTIVE!"… but then you have to go back by hand to figure out whether the LTR activity is random noise, a minor contributor to gene expression, creating an alternative protein, or the sole promoter for the gene.. A review was just published that consolidates a lot of what we know about ERV LTRs and human genes.. ...
Plays a role in constitutive splicing and can modulate the selection of alternative splice sites. Represses the splicing of MAPT/Tau exon 10.
MIT Professor Susan Lee Lindquist, a member and former director of the Whitehead Institute, and one of the nations most lauded scientists, has died of cancer at age 67. She made invaluable contributions to the study of protein folding, demonstrating that alternative protein conformations can have profound and unexpected influences.
As this eMedTV segment explains, there are many different alternatives to Kazano (alogliptin and metformin), including other oral drugs, insulin, and lifestyle changes. This page explains these options in detail with specific examples.
The European Securities and Markets Authority (ESMA) has published a new Questions and Answers (Q&A) document, comprising six questions, on the implementation of its Guidelines on the Alternative Performance Measures for listed issuers.
The blastp of the GRMZM2G012966 model gives the most complete alignment to lyce1, so that model is likely the most correct model. The lyce1 alignment for Models 1 and 2 are truncated at the 3 end, suggesting that the models have a framshift mutation somewhere in exon 8. Models 1 and 2 do provide some additional information, however. The 3 end of the sequence contains a protein kinase-like (PKc_like superfamily) region, which suggests that both models should in fact be split up into two different genes. This means that the cDNA (gb,BT037027.1; GENE ID: 100216601 LOC100216601 ) is not part of the lcye1 gene, confirming that the gene is confined between coordinates 82,726 and 85,759 (or 138882727 and 138885760 in the Reference Genome).. The blastx results of Model 2 show that exons 8 and 9 (the ones not contained in Model 1 or GRMZM2G012966) aligns to lyce1 (see reading frame +1 between 2000 and 2500 of the query). This supports the idea that an alternative gene model involving alternatively ...
Myc-DDK-tagged ORF clone of Homo sapiens RAD52 motif 1 (RDM1), transcript variant 3 as transfection-ready DNA - 10 µg - OriGene - cdna clones
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This is perhaps the most difficult part of cognitive restructuring because the practitioner may be able to see the alternatives, but needs to facilitate the individual client to arrive at these alternatives using one or more of the techniques outlined below. The alternative interpretation or constructive idea is phrased as a hypothesis, i.e. a theory or assumption for which we need to come to a conclusion about how accurate it is compared to the initial interpretations and ideas, and/or how helpful it may be in changing the way we feel and behave. At this stage, we may choose not to judge or add value to the alternatives until the next step of cognitive restructuring when we test them for accuracy and helpfulness. Remember, the objective is not to show that we are right and the other person is wrong but to show that there are other options that could be considered. Prompt sheet Using a prompt sheet (Figure 25.4), the client could write down their key thoughts (my interpretations and ideas are ...
It is reasonable to obtain a histological diagnosis before treating patients who have pancreatic masses and are unsuitable or unwilling to undergo surgery.
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DB-ID: Database ID of variant, grouping multiple observations of the same variant together, starting with the HGNC gene symbol, followed by an underscore (_) and a six digit number (e.g. DMD_012345). _000000 is used for variants where DNA was not analysed (change predicted from RNA analysis), variants seen in animal models or variants not seen in humans but functionally tested in vitro ...
DB-ID: Database ID of variant, grouping multiple observations of the same variant together, starting with the HGNC gene symbol, followed by an underscore (_) and a six digit number (e.g. DMD_012345). _000000 is used for variants where DNA was not analysed (change predicted from RNA analysis), variants seen in animal models or variants not seen in humans but functionally tested in vitro ...
DB-ID: Database ID of variant, grouping multiple observations of the same variant together, starting with the HGNC gene symbol, followed by an underscore (_) and a six digit number (e.g. DMD_012345). _000000 is used for variants where DNA was not analysed (change predicted from RNA analysis), variants seen in animal models or variants not seen in humans but functionally tested in vitro ...
My work at ScHARR has concentrated around undertaking and developing methods for economic evaluations alongside controlled trials. Whilst the main focus of this work has been pre-hospital and emergency care, I have undertaken evaluations in numerous other areas. A separate stream of work is examining the measurement and valuation of health care benefits. This is focusing on alternatives to, and extensions of, the standard QALY model.. ...
Sapandeep Kaur and Isha Thakur (Correspondence: Acharya KK, [email protected]), A compilation and categorization of alternative splicing resources; In: Startbioinfo; 30 June 2012, http://www.startbioinfo.com/alternative splicing resources/" ...
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The protein encoded by this gene is similar to the protein transgelin, which is one of the earliest markers of differentiated smooth muscle. The specific function of this protein has not yet been determined, although it is thought to be a tumor suppressor. Multiple transcript variants encoding different isoforms have been found for this gene. [provided by RefSeq, Mar 2013 ...
(KudoZ) English to French translation of alternative splicing, a process that yields different protein products [DNA - Science (general) (Medical)].
The availability of meat-free products has risen in recent years, but new research shows this seemingly healthy alternative isnt all it may seem.
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Learn more about Alternative Birthing: Is It Safe? at Grand Strand Medical Center Today, most women give birth in hospitals, under the care of obstetricians. But...
-When is it appropriate to use an informal assessment? When would a formal assessment be more appropriate? -Reflect on a time when an alternative assessment was utilized successfully. Provide a description of the assessment and.
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Liao, P., Yu, D., Li, G., Tan, F.Y., Tuck, W.S., Jia, L.S., Yeow, L.C. (2007). A smooth muscle Cav1.2 calcium channel splice variant underlies hyperpolarized window current and enhanced state-dependent inhibition by nifedipine. Journal of Biological Chemistry 282 (48) : 35133-35142. [email protected] Repository. https://doi.org/10.1074/jbc. ...
The receptor for advanced glycosylation end products (RAGE) is a multiligand receptor involved in diverse cell signaling pathways. Previous studies show that this gene expresses several splice variants in human, mouse, and dog. Alternative splicing (AS) plays an important role in expanding transcriptomic and proteomic diversity, and it has been related to disease. AS is also one of the main evolutionary mechanisms in mammalian genomes. However, limited information is available regarding the AS of RAGE in a wide context of mammalian tissues. In this study, we examined in detail the different RAGE mRNAs generated by AS from six mammals, including two primates (human and monkey), two artiodactyla (cow and pig), and two rodentia (mouse and rat) in 6-18 different tissues including fetal, adult, and tumor. By nested reverse transcription-polymerase chain reaction (RT-PCR) we identified a high number of splice variants including noncoding transcripts and predicted coding ones with different potential ...
LKB1 was discovered as a tumour suppressor mutated in Peutz-Jeghers syndrome, and is a gene involved in cell polarity as well as an upstream protein kinase for members of the AMP-activated protein kinase family. We report that mammals express two splice variants caused by alternate usage of 3′-exons. LKB1L is the previously described form, while LKB1S is a novel form in which the last 63 residues are replaced by a unique 39-residue sequence lacking known phosphorylation (Ser431) and farnesylation (Cys433) sites. Both isoforms are widely expressed in rodent and human tissues, although LKB1S is particularly abundant in haploid spermatids in the testis. Male mice in which expression of Lkb1S is knocked out are sterile, with the number of mature spermatozoa in the epididymis being dramatically reduced, and those spermatozoa that are produced have heads with an abnormal morphology and are non-motile. These results identify a previously undetected variant of LKB1, and suggest that it has a crucial ...
A novel isoform ratio switch of the polypyrimidine tract binding proteins profile, publications, research topics, and co-authors
In this study researchers from the Loma Linda University School of Medicine show for the first time that like Survivin, the Survivin splice variants are also exosomally packaged in the breast cancer patients sera, mimicking the survivin splice variant pattern that we also report in breast cancer tissues. Differential
Alternative splicing of a pair of mutually exclusive exons (exon 37a and 37b) of the P/Q-type Ca2+ channels produces two different splice variants in the EF-hand region, namely Cav2.1[EFa] and Cav2.1[EFb] channels. Using isoform-specific antibodies against Cav2.1[EFa] and Cav2.1[EFb] channels, we show that Cav2.1[EFa] and Cav2.1[EFb] channels are differentially localized in subcellular compartments of hippocampal, cerebellar and cortical neurons. Cav2.1[EFb] channels show somatic, proximal and distal dendritic localization while Cav2.1[EFa] channels are expressed in the cell bodies, proximal dendrites as well as presynaptic terminals. The distinct subcellular localization of Cav2.1[EFa] and Cav2.1[EFb] channels suggests compartmentalized roles of voltage-gated Ca2+ channels in neurotransmitter release and generation of synaptic plasticity. In addition, a yeast-two-hybrid screen was performed to find potential interacting proteins with the EF-hand of the Cav2.1[EFa] channel. The screen reveals ...
Chromatin modification influences gene expression by either repressing or activating genes, depending on the specific histone mark. Chromatin structure can also influence alternative splicing of transcripts; however, the mechanisms by which epigenetic marks influence splicing are poorly understood. A report in the current issue of the JCI highlights the biological importance of the coordinated control of alternative pre-mRNA splicing by chromatin structure and transcriptional elongation. Yuan et al. found that mutation of the histone methyl transferase SEDT2 affects alternative splicing fates of several key regulatory genes, including those involved in Wnt signaling. As a consequence, loss of SEDT2 in the intestine aggravated Wnt/β-catenin signaling effects, thereby leading to colorectal cancer.. ...
Alternative pre-mRNA splicing in Drosophila. D. Rio - PI Alternative pre-mRNA splicing is an important mechanism for regulating gene expression in metazoans. In...
Tissue factor (TF) triggers blood coagulation and is translated from two mRNA splice isoforms, encoding membrane-anchored full-length TF (flTF) and soluble alternatively-spliced TF (asTF). The complete knockout of TF in mice causes embryonic lethality associated with failure of the yolk sac vasculature. Although asTF plays roles in postnatal angiogenesis, it is unknown whether it activates coagulation sufficiently or makes previously unrecognized contributions to sustaining integrity of embryonic yolk sac vessels. Using gene knock-in into the mouse TF locus, homozygous asTF knock-in (asTFKI) mice, which express murine asTF in the absence of flTF, exhibited embryonic lethality between day 9.5 and 10.5. Day 9.5 homozygous asTFKI embryos expressed asTF protein, but no procoagulant activity was detectable in a plasma clotting assay. Although the α-smooth-muscle-actin positive mesodermal layer as well as blood islands developed similarly in day 8.5 wild-type or homozygous asTFKI embryos, ...
The BY4741 strain used in (Nagalakshmi et al. 2008) was used in this study. RNA-Seq was performed using the protocol developed in (Nagalakshmi et al. 2008), further described in (Nagalakshmi et al. 2010) and (Waern et al. 2011), and using the modifications developed by (Parkhomchuk et al. 2009) to generate strand-specific reads.. Analysis was performed on custom software developed in-house using BowTie (Langmead et al. 2009) to map reads to the S288C reference genome available on SGD, downloaded on May 17, 2010. Python, NumPy, SciPy, and matplotlib were used to further process the data. The softwares source code is available (Saccharomyces Genome Database). Of note, to maximize the information gleaned, unmappable reads were trimmed by four bases from the 3′ end and remapping was attempted; this was done iteratively until only 28 bp remained, at which point the read was considered unmappable. This end trimming typically doubled or more the number of mappable reads.. Expression levels were ...
We described novel renin isoforms identified in mice different from previous reports. Bona fide alternative transcription is initiated from AREx1a localized in the first intron of the renin gene as shown previously,8-10 with no identical sequence for the mice with and without a duplication of the renin gene. We also demonstrated the promoter activity of 5′ of AREx1a by promoter activity assays (Figure S2A and S2B). Demonstration of promoter activity and confirmation by RT-PCR excluded the possibility of RACE artifacts. Because both adrenal glands and kidneys play pivotal roles in fluid and electrolyte homeostasis, the expression of alternative isoforms of renin is key to tissue-specific generation of A-II. Our quantitative analyses using RT-PCR showed that relative abundances of alternate transcripts were ≈10% of classical renin transcripts in kidneys (Figure 2A).. The identification of alternative renin isoforms raises several interesting questions on local A-II formation.10,12,13 ...
Alternative splicing is thought to occur in 41-60% of genes in the human genome (Black, 2003; Herbert, 2004). Pre‐mRNAs can give rise to multiple protein isoforms with different functions and these variations contribute to protein diversity (Black, 2003). Alternative splicing also provides an additional regulatory mechanism by which vertebrates can control the expression of tissue‐specific or developmental stage‐specific protein isoforms. RNA‐binding proteins that regulate alternative splicing bind to sequence‐specific elements in the pre‐mRNA to enhance or repress inclusion of alternative exons. Aberrant regulation of alternative splicing can cause the expression of inappropriate splicing patterns leading to human disease (Faustino and Cooper, 2003). An example of a disease that alters the function of RNA‐binding proteins to cause misregulated alternative splicing is myotonic dystrophy (DM). Interestingly, the effects on splicing in DM1 are thought to be limited to specific ...
Alternative splice variants of ET receptors have been reported but to date these variants either show little or no change in binding characteristics and their physiological or pathophysiological significance is unclear. The following is intended to be a guide only because the field has not developed sufficiently with unequivocal quantitative evidence for significant expression and function in native tissues rather than artificial cell lines, to make any firm recommendation for classification.. The existence of alternative splice variants of the ETB receptor in human and porcine tissue has been reported. A variant human ETB receptor that results in a 10-aa increase in the length of the second cytoplasmic domain has been described (Shyamala et al., 1994). Messenger RNA measured by reverse transcription-polymerase chain reaction in a limited number of human tissues was found only in low abundance in human brain (which expresses one of the highest densities of ETB receptors) as well as the heart, ...
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-binding protein that acts as a regulator of alternative pre-mRNA splicing. Involved in apoptotic cell death through the regulation of the apoptotic factor BCL2L1 isoform expression. Modulates the ratio of proapoptotic BCL2L1 isoform S to antiapoptotic BCL2L1 isoform L mRNA expression. When overexpressed, stimulates proapoptotic BCL2L1 isoform S 5-splice site (5-ss) selection, whereas its depletion caused the accumulation of antiapoptotic BCL2L1 isoform L. Promotes BCL2L1 isoform S 5-ss usage through the 5-CGGGCA-3 RNA sequence. Its association with LUC7L3 promotes U1 snRNP binding to a weak 5 ss in a 5-CGGGCA-3-dependent manner. Binds to the exonic splicing enhancer 5-CGGGCA-3 RNA sequence located within exon 2 of the BCL2L1 pre-mRNA. Also involved in the generation of an abnormal and truncated splice form of SCN5A in heart failure.
A Ribonucleic acid (RNA) is a molecule found in all cells, comprised of many individual units of nucleic acid. It differs from DNA (deoxyribonucleic acid) in that it only contains a single, not double strand, and substitutes uracil for thymine. The sugar backbone of RNA is also composed of ribose (DNA contains deoxyribose). RNAs fall into several different categories, depending on function. The primary role of mRNA in is to transfer a copy of the information coded in DNA to a ribosome to be expressed as a protein, using a form of RNA known as messenger RNA (mRNA). mRNA in eukaryotes undergoes spicing after transcription from DNA to remove introns or to use alternative splicing to create a different gene product. Alternatively-spliced transcripts can also express the same protein, but at different levels, due to the removal or addition of regulatory sequences. The main role of tRNA, or transfer RNA is to carry an amino acid to the mRNA (while the mRNA is in the ribosome) during translation 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 ...
Page: 1 of 1 Select page: 1 Important note: For a particular human or mouse gene, there may be multiple splice variants represented by different accession numbers. Please make sure you are selecting the right Product ID representing the specific splice variant (or accession number) that you are interested in. If you need clones whose accession numbers are not in the list, please email [email protected] with your specific needs.. ...
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 ...
SIRT1 is a pleiotropic protein that plays critical and multifunctional roles in metabolism, senescence, longevity, stress-responses, and cancer, and has become an important therapeutic target across a range of diseases. Recent research demonstrated that SIRT1 pre-mRNA undergoes alternative splicing to produce different isoforms, such as SIRT1 full-length and SIRT1-∆Exon8 variants. Previous studies revealed these SIRT1 mRNA splice variants convey different characteristics and functions to the protein, which may in turn explain the multifunctional roles of SIRT1. However, the mechanisms underlying the regulation of SIRT1 alternative splicing remain to be elucidated. Our objective is to search for new pathways that regulate of SIRT1 alternative splicing. Here we describe experiments showing that HuR and TIA1/TIAL1, two kinds of RNA-binding proteins, were involved in the regulation of alternative splicing of SIRT1 pre-mRNA under normal and stress circumstances: HuR increased SIRT1-∆Exon8 by promoting
Alternative splicing in eukaryotes plays an important role in regulating gene expression by selectively including alternative exons. A wealth of information has been accumulated that explains how alternative exons are selected in a developmental stage- or tissue-specific fashion. However, our knowledge of how cells respond to environmental changes to alter alternative splicing is very limited. For example, although a number of alternative exons have been shown to be regulated by calcium level alterations, the underlying mechanisms are not well understood. As calcium signaling in neurons plays a crucial role in essential neuronal functions such as learning and memory formation, it is important to understand how this process is regulated at every level in gene expression. The significance of the dynamic control of alternative splicing in response to changes of calcium levels has been largely unappreciated. In this communication, we will summarize the recent advances in calcium signaling-mediated
Transcript Variant: This variant (4) includes alternate exons in its 5 and central regions, and uses an alternate splice site in its central region, compared to variant 1. This variant is represented as non-coding because the use of the supported translational start codon, as used in variant 1, renders the transcript a candidate for nonsense-mediated mRNA decay (NMD ...
Developmental processes require precise spatial and temporal regulation of gene expression. Accordingly, developmental biologists have always been at the forefront of gene expression analysis, and recombinant DNA techniques such as transgenic and knockout models have greatly contributed to elucidation of developmental pathways and networks. Traditionally, these studies have focused on transcription factors and repressors that regulate the timing and strength of transcription. Recently, new regulatory mechanisms have emerged, such as post-transcriptional regulation by microRNAs and co-transcriptional regulation by alternative pre-mRNA splicing.. Alternative splicing is a pre-mRNA maturation process that consists of the removal or inclusion of certain alternative exons to produce different transcripts from one genomic locus [1, 2]. Alternative splicing is now known to be prevalent in advanced eukaryotes. In humans, recent reports show that more than 98% of multi-exonic pre-mRNAs are alternatively ...
Check out the November 2016 issue of Prepared Foods, featuring our cover story on alternative proteins, along with features on dietary minerals, Hispanic-style food trends, and more!
Alternative splicing is the process by which an exon is preferentially included or excluded from an mRNA transcript. Recent global sequencing studies have shown that |95% of the transcriptome undergoes some form of alternative splicing. Such regulation often alters protein isoform expression, as is especially apparent in T cells of the immune system that change their expression of RNA and protein according to signaling cues. The focus of this thesis is on one alternative exon in the pre-mRNA of transcription factor LEF1 and its regulation by the splicing factor CELF2. LEF1 is crucial for T cell function as it upregulates the expression of TCRα. Upon signal induction in T-cells, CELF2 promotes the inclusion of exon 6 in LEF1 (LEF1-E6) in the final mRNA transcript. This increase in LEF-E6 inclusion generates an isoform of LEF1 that is preferentially active in promoting transcription of TCRα. CELF2 regulates LEF1-E6 inclusion upon stimulation by increasing its binding to two conserved elements (USE60 and
Alternative protein import pathways into the peroxisomal matrix 12:00-13:20 Lunch (finger food & cake) 13:20-13:40 Marco Guerreiro (Begerow) ...
I am 100% with Larry on this one. The fact is, ALL of the transcript detection employed in these omics studies is not quantitative. Sure, authors like to pretend that it is, but no, it isnt. The question is simple and the way to answer it is very straightforward. But very labor-intensive. First, forget RNA. Protein-coding gene expression is not transcription. Its translation. So, make and purify Ab against every exon from ,50 genes known to have tissue-specific isoforms. And from ,50 genes that we dont know this about (including some, like HSA and actin, where we know fir sure that there are no splice isoforms at all). After that, only about 10,000 of Western runs ought to tell whats real and whats not. It will also provide an experimental test for the predictions made by paper biochemists cracking the enigma codes. But, of course, thats too difficult and not sexy to actually be funded and be done.. ReplyDelete ...
... ,The binding specificity and signaling of the members of the GPCR family are known to be modified by alternative splicing--which has important implications for drug research. With GPCR SpliceArrays you can perform a classical expression profiling and at the same time detect the different alternative,biological,biology supply,biology supplies,biology product
Background and represent two major splice variations of human metalloproteinase-disintegrin 12 mRNA, which differ in their 3-untranslated regions (3UTRs). transfecting cells with miRNA hairpin inhibitors. Results Transfection of miR-29b/c mimics decreased mRNA levels in Amount159PTestosterone levels and BT549 cells highly, whereas amounts had been not really transformed. mRNA. Significantly, both miR-29b/c and miR-200b/c highly reduced continuous condition amounts of ADAM12-M proteins in all breasts cancer tumor cell lines examined. miR-29b/c.. Read More. ...
Background and represent two major splice variations of human metalloproteinase-disintegrin 12 mRNA, which differ in their 3-untranslated regions (3UTRs). transfecting cells with miRNA hairpin inhibitors. Results Transfection of miR-29b/c mimics decreased mRNA levels in Amount159PTestosterone levels and BT549 cells highly, whereas amounts had been not really transformed. mRNA. Significantly, both miR-29b/c and miR-200b/c highly reduced continuous condition amounts of ADAM12-M proteins in all breasts cancer tumor cell lines examined. miR-29b/c.. Read More. ...
Genomatix Software GmbH announced today that it will extend the leading position of its gene chip compatible products further by a new version of ChipInspector, which will be specifically geared towards analysis of the new exon arrays.
In this thesis, I describe investigations into the evolution of splicing in mammals. I first investigate a small class of alternative splicing events, tandem splice sites, and show how they are used to introduce and remove ...
Mutations of an alternative splice donor site located within the gag region has previously been shown to broaden the pathogenic potential of the T-lymphomagenic gammaretrovirus Moloney murine leukemia virus, while the equivalent mutations in the erythroleukemia inducing Friend murine leukemia virus seem to have no influence on the disease-inducing potential of this virus. In the present study we investigate the splice pattern as well as the possible effects of mutating the alternative splice sites on the oncogenic properties of the B-lymphomagenic Akv murine leukemia virus. By exon-trapping procedures we have identified a novel gammaretroviral exon, resulting from usage of alternative splice acceptor (SA) and splice donor (SD) sites located in the capsid region of gag of the B-cell lymphomagenic Akv murine leukemia virus. To analyze possible effects in vivo of this novel exon, three different alternative splice site mutant viruses, mutated in either the SA, in the SD, or in both sites, respectively,
Abstract: Fish meal is the protein source traditionally used in aquaculture diets, yet it is a limited resource and is expensive. Alternative protein sources can lower the cost of aquaculture diets, reduce the amount of wild fish used as protein, and potentially reduce the nutrient levels in effluent waste. Soybean meal, poultry-by-product meal, and meat-and-bone meal have high protein contents and amino acid profiles similar to that of fish meal. They are readily available and less expensive than fish meal. In a previous study, black sea bass fed diets with up to 60% of the fish meal replaced by soybean meal showed no significant differences in growth rates compared to those fed a control FM diet (Alam et al., unpublished data). Based on these results, five diets were formulated that replaced fish meal protein by soybean meal at 0, 60, 70, 80, 90 and 100%. In addition, a diet with 60% of the fish meal replaced by poultry by-product meal and a diet with 30% of the fishmeal replaced by ...
8-Oxoguanine glycosylase also known as OGG1 is a DNA glycosylase enzyme that, in humans, is encoded by the OGG1 gene. It is involved in base excision repair. It is found in bacterial, archaeal and eukaryotic species. OGG1 is the primary enzyme responsible for the excision of 8-oxoguanine (8-oxoG), a mutagenic base byproduct that occurs as a result of exposure to reactive oxygen species (ROS). OGG1 is a bifunctional glycosylase, as it is able to both cleave the glycosidic bond of the mutagenic lesion and cause a strand break in the DNA backbone. Alternative splicing of the C-terminal region of this gene classifies splice variants into two major groups, type 1 and type 2, depending on the last exon of the sequence. Type 1 alternative splice variants end with exon 7 and type 2 end with exon 8. One set of spliced forms are designated 1a, 1b, 2a to 2e. All variants have the N-terminal region in common. Many alternative splice variants for this gene have been described, but the full-length nature for ...
SR proteins are a conserved family of proteins involved in RNA splicing. SR proteins are named because they contain a protein domain with long repeats of serine and arginine amino acid residues, whose standard abbreviations are "S" and "R" respectively. SR proteins are ~200-600 amino acids in length and composed of two domains, the RNA recognition motif (RRM) region and the RS domain. SR proteins are more commonly found in the nucleus than the cytoplasm, but several SR proteins are known to shuttle between the nucleus and the cytoplasm. SR proteins were discovered in the 1990s in Drosophila and in amphibian oocytes, and later in humans. In general, metazoans appear to have SR proteins and unicellular organisms lack SR proteins. SR proteins are important in constitutive and alternative pre-mRNA splicing, mRNA export, genome stabilization, nonsense-mediated decay, and translation. SR proteins alternatively splice pre-mRNA by preferentially selecting different splice sites on the pre-mRNA strands ...
Zheng X, Cho S, Moon H, Loh TJ, Oh HK, Green MR, Shen H. Polypyrimidine tract binding protein inhibits IgM pre-mRNA splicing by diverting U2 snRNA base-pairing away from the branch point. RNA. 2014 Apr; 20(4):440-6 ...
The adenovirus major late transcription unit (MLTU) is an example of a complex alternatively spliced gene, in which more than 15 different 3 splice sites can be joined to a common 5 splice site. Maturation of the full repertoire of possible mRNAs requires late viral protein synthesis and occurs only at late stages of the infectious cycle (16-24 hpi). We are trying to decipher the mechanisms regulating alternative 3 splice site choice during the infectious cycle. Therefore, we examined the splicing activity of several 3 splice sites from the MLTU in vitro in nuclear extracts prepared from adenovirus infected cells (Ad NE) and from uninfected cells. The results suggest that pre-mRNAs with "weak" 3 splice sites (short, atypical polypyrimidine tracts) are activated and pre-mRNAs with long, prototypical polypyrimidine tracts are repressed in Ad NE. In fact, our data show a reciprocal correlation between the strength of a polypyrimidine tract, defined by its affinity for U2AF65K in vitro, and the ...
The Consensus Document on Alternatives to Allogenic Blood Transfusion (AABT) has been drawn up by a panel of experts from 5 scientific societies. The Seville Consensus Document on Alternatives to Allogenic Blood Transfusion
In this study, we describe the clinical features and provide experimental analyses of a novel point mutation affecting the penultimate nucleotide of the first exon of the HBA2 (HBA2: c.94A,G) gene identified in a 26-year-old female who also carries a heterozygous Hb E (HBB: c.79G,A) variant. The aim of the study was to investigate the impact of this point mutation on the transcriptional activity of the HBA2 gene using a combination of an initial in silico prediction followed by in vitro mutagenesis and transcriptional activity assessment. The analyses revealed that the HBA2: c.94A,G point mutation causes the activation of a cryptic splice site located 49bp upstream of the exon1-intron1 boundary in both HBA2 long and short isoforms, thus generating a frameshift and a premature termination codon between codons 48 and 49 in the second exon. A rapid degradation of the aberrantly spliced transcripts by the nonsense mediated decay (NMD) surveillance system is highly indicative of an a-thalassemia ...

Alternative Splicing ModesAlternative Splicing Modes

Are you looking for more information on alternative splicing modes? If so, read on to learn more about this basic genetics ... In this alternative splicing mode, a sequence may be simply retained or spliced out as an intron. This differs from the exon ... Alternative Donor Site. In this mode, a donor site, an alternative 5 splice junction, is used. This changes the 3 boundary of ... Alternative splicing, also referred to as differential splicing, is a process where the RNA exons of the RNA that is produced ...
more infohttp://www.brighthub.com/science/genetics/articles/89429.aspx

Alternative splicingAlternative splicing

Protein for which at least two isoforms exist due to distinct pre-mRNA splicing events. ...
more infohttp://www.uniprot.org/keywords/25

Alternative splicing - WikipediaAlternative splicing - Wikipedia

Research Group dealing with alternative Splicing issues and mis-splicing in human diseases Alternative Splicing of ion channels ... Since then, alternative splicing has been found to be ubiquitous in eukaryotes. The "record-holder" for alternative splicing is ... These databases are useful for finding genes having pre-mRNAs undergoing alternative splicing and alternative splicing events. ... A General Definition and Nomenclature for Alternative Splicing Events at SciVee AStalavista (Alternative Splicing landscape ...
more infohttps://en.wikipedia.org/wiki/Alternative_splicing

Alternative splicing: current perspectives.  - PubMed - NCBIAlternative splicing: current perspectives. - PubMed - NCBI

Do similar forces act on all types of alternative splicing? Are the products generated by alternative splicing functional? Why ... Alternative splicing: current perspectives.. Kim E1, Goren A, Ast G.. Author information. 1. Department of Human Molecular ... Alternative splicing is a well-characterized mechanism by which multiple transcripts are generated from a single mRNA precursor ... By allowing production of several protein isoforms from one pre-mRNA, alternative splicing contributes to proteomic diversity. ...
more infohttps://www.ncbi.nlm.nih.gov/pubmed/18081010?dopt=Abstract

Alternative splicing annotation project - WikipediaAlternative splicing annotation project - Wikipedia

Alternative Splicing Annotation Project (ASAP) is a database for alternative splicing data. The purpose of this project was to ... Lee, C., Atanelov, L., Modrek, B., & Xing, Y. (2003). ASAP: the alternative splicing annotation project. Nucleic Acids Research ... analysis and comparative genomics of alternative splicing in 15 animal species". Nucleic Acids Res. England. 35 (Database issue ... AspicDB RNA splicing Kim, Namshin; Alekseyenko Alexander V; Roy Meenakshi; Lee Christopher (Jan 2007). "The ASAP II database: ...
more infohttps://en.wikipedia.org/wiki/Alternative_splicing_annotation_project

Alternative Spliced Transcripts as Cancer MarkersAlternative Spliced Transcripts as Cancer Markers

This process can lead to transcript diversification through the phenomenon of alternative splicing. Alternative splicing can ... Alternative Spliced Transcripts as Cancer Markers. Otavia L. Caballero,2 Sandro J. de Souza,2 Ricardo R. Brentani,1,2 and ... The effect of alternative splicing in expanding protein repertoire might partially underlie the apparent discrepancy between ... Many cancer-associated genes, such as CD44 and WT1 are alternatively spliced. Variation of the splicing process occurs during ...
more infohttps://www.hindawi.com/journals/dm/2001/184856/abs/

Alternative splicing - wikidocAlternative splicing - wikidoc

There are four known modes of alternative splicing: *Alternative selection of promoters: this is the only method of splicing ... Study on alternative splicing and complexity. *Stamms-lab.net: Research Group dealing with alternative Splicing issues and mis- ... Alternative splicing is the variation of the splicing process in which the exons of the primary gene transcript, the pre-mRNA, ... Alternative selection of cleavage/polyadenylation sites: this is the only method of splicing which can produce an alternative C ...
more infohttps://www.wikidoc.org/index.php/Alternative_splicing

GitHub - HussainAther/awesome-alternative-splicing: Alternative splicing resourceGitHub - HussainAther/awesome-alternative-splicing: Alternative splicing resource

Contribute to HussainAther/awesome-alternative-splicing development by creating an account on GitHub. ... awesome-alternative-splicing. What is this?. This is a resource for software and information about alternative splicing. ... Alternative 5 splice site (A5SS): An alternative 5 splice junction (donor site) is used that changes the 3 boundary of the ... Alternative 3 splice site (A3SS): An alternative 3 splice junction (acceptor site) is used that changes the 5 boundary of ...
more infohttps://github.com/HussainAther/awesome-alternative-splicing

Alternative splicing, an important mechanism for cancer | EurekAlert! Science NewsAlternative splicing, an important mechanism for cancer | EurekAlert! Science News

Therefore, the study of alternative splicing opens new doors in the research to cure cancer and may provide new alternatives to ... Alternative splicing, an important mechanism for cancer Scientists discover several alterations in this cellular process with ... "Changes in alternative splicing provide cancer with new ways in which it can escape fine cellular regulation. ... "With this new study, we have discovered that changes in alternative splicing that occur in cancer impact protein functions in a ...
more infohttps://www.eurekalert.org/pub_releases/2017-09/spmd-asa092117.php

Global regulation of alternative splicing during myogenic differentiation.  - PubMed - NCBIGlobal regulation of alternative splicing during myogenic differentiation. - PubMed - NCBI

Global regulation of alternative splicing during myogenic differentiation.. Bland CS1, Wang ET, Vu A, David MP, Castle JC, ... Recent genome-wide analyses have elucidated the extent of alternative splicing (AS) in mammals, often focusing on comparisons ... C) Summary of the different types of validated splicing transitions included within the data set of 117 splicing transitions. ( ... Clusters of splicing transitions with similar temporal patterns exhibit enrichment of specific motifs. Splicing transitions ...
more infohttps://www.ncbi.nlm.nih.gov/pubmed/20634200

Alternative splicing | Journal of Cell ScienceAlternative splicing | Journal of Cell Science

How alternative splicing affects membrane-trafficking dynamics R. Eric Blue, Ennessa G. Curry, Nichlas M. Engels, Eunice Y. Lee ... miRNA targeting and alternative splicing in the stress response - events hosted by membrane-less compartments Mariya M. ... CCAR-1 affects hemidesmosome biogenesis by regulating unc-52/perlecan alternative splicing in the C. elegans epidermis Rong Fu ... Summary: Loss of CCAR-1 function during C. elegans embryogenesis results in dysregulated alternative splicing of unc-52 (the ...
more infohttp://jcs.biologists.org/keyword/alternative-splicing

JCVI: Gene and Alternative Splicing Annotation With AIRJCVI: Gene and Alternative Splicing Annotation With AIR

... such as alternative splicing. We present a methodology for the automated annotation of genes and their alternatively spliced ... and combines the traditionally distinct gene annotation and alternative splicing detection processes in a comprehensive and ... At the core of the method is the splice graph, a compact representation of a gene, its exons, introns, and alternatively ... spliced isoforms. The putative transcripts are enumerated from the graph and assigned confidence scores based on the strength ...
more infohttp://www.jcvi.org/cms/publications/listing/abstract/article/gene-and-alternative-splicing-annotation-with-air/

Frontiers | Depolarization-Mediated Regulation of Alternative Splicing | NeuroscienceFrontiers | Depolarization-Mediated Regulation of Alternative Splicing | Neuroscience

... we will summarize how splicing regulators change and affect alternative splicing in this process. We will also discuss a novel ... we will summarize how splicing regulators change and affect alternative splicing in this process. We will also discuss a novel ... The significance of the dynamic control of alternative splicing in response to changes of calcium levels has been largely ... The significance of the dynamic control of alternative splicing in response to changes of calcium levels has been largely ...
more infohttps://www.frontiersin.org/articles/10.3389/fnins.2011.00141/full

alternative splicing | Biochemical Society Transactionsalternative splicing | Biochemical Society Transactions

Tra2 protein biology and mechanisms of splicing control Andrew Best, Caroline Dalgliesh, Mahsa Kheirollahi-Kouhestani, Marina ... Functional impact of splice isoform diversity in individual cells Karen Yap, Eugene V. Makeyev ...
more infohttp://www.biochemsoctrans.org/keyword/alternative-splicing

Genomic Research - RNA Alternative Splicing, Genetic Disorders and Protein SynthesisGenomic Research - RNA Alternative Splicing, Genetic Disorders and Protein Synthesis

RNA alternative splicing was first noticed in adenoviruses in the 1970s. The researchers noticed that adenoviruses produced two ... Find out more about the role of RNA and RNA alternative splicing in protein synthesis and genetic disorders. ... Importance of RNA Alternative Splicing. RNA alternative splicing enables genetic efficiency and genetic diversity. On the ... RNA Alternative Splicing. First let us understand what splicing is. DNA directs the synthesis or production of RNA. This is ...
more infohttps://www.brighthub.com/science/genetics/articles/47494.aspx

alternative splicing, a process that yields different protein productsalternative splicing, a process that yields different protein products

English to French translation of alternative splicing, a process that yields different protein products [DNA - Science (general ... alternative splicing, a process that yields different protein products. However, its now believed that the incredible ... alternative splicing, a process that yields different protein products. French translation: épissage alternatif. ... "alternative splicing" (a process that yields different protein products* from the same gene),. ...
more infohttps://www.proz.com/kudoz/english_to_french/science_general/885970-alternative_splicing_a_process_that_yields_different_protein_products.html

Regulation of CD45 alternative splicing by HNRPLLRegulation of CD45 alternative splicing by HNRPLL

Research Topics about Regulation of CD45 alternative splicing by HNRPLL ... alternative splicing*antigens*formal social control*tyrosine*memory*antigen receptors*signal transduction*ribonucleoproteins* ... Regulation of CD45 alternative splicing by HNRPLL. Summary. Principal Investigator: Anjana Rao ... Regulation of CD45 alternative splicing by heterogeneous ribonucleoprotein, hnRNPLL. Shalini Oberdoerffer. Department of ...
more infohttp://www.labome.org/grant/r01/ai/regulation/of/regulation-of-cd45-alternative-splicing-by-hnrpll-8436128.html

Sandwalk: Debating alternative splicing (part II)Sandwalk: Debating alternative splicing (part II)

This suggests that theres exquisite regulation of alternative splicing due to splicing factors. Splicing errors: Most of the ... During alternative splicing, which occurs after transcription and before translation, introns are removed and exons are spliced ... I asked: How do you explain complexity if you through away alternative splicing? I didnt say that alternative slicing was my ... Most of the labs that work on these splice variants are proponents of massive alternative splicing. They operate on the ...
more infohttps://sandwalk.blogspot.com/2017/06/debating-alternative-splicing-part-ii.html?showComment=1498417208403

Neuronal Signaling through Alternative Splicing: Some Exons CaRRE... | Science SignalingNeuronal Signaling through Alternative Splicing: Some Exons CaRRE... | Science Signaling

Neuronal Signaling through Alternative Splicing: Some Exons CaRRE... Message Subject. (Your Name) has forwarded a page to you ...
more infohttps://stke.sciencemag.org/content/2001/94/pe2/tab-pdf

Comparative Cross-Species Alternative Splicing in Plants | Plant PhysiologyComparative Cross-Species Alternative Splicing in Plants | Plant Physiology

... splice donor sites, alternative 3′ splice acceptor sites, and intron retention. AS patterns are represented by (top and bottom ... alternative splice sites. Taken together, these results indicate that EPGA can faithfully report genome-wide splicing events ... Comparative Cross-Species Alternative Splicing in Plants Message Subject (Your Name) has sent you a message from Plant ... Comparative Cross-Species Alternative Splicing in Plants. Hadas Ner-Gaon, Noam Leviatan, Eitan Rubin, Robert Fluhr ...
more infohttp://www.plantphysiol.org/content/144/3/1632

JCI -
Histone methyltransferase SETD2 modulates alternative splicing to inhibit intestinal tumorigenesisJCI - Histone methyltransferase SETD2 modulates alternative splicing to inhibit intestinal tumorigenesis

Mechanistic characterizations indicated that SETD2 downregulation affects the alternative splicing of a subset of genes ...
more infohttps://www.jci.org/articles/view/94292/pdf

JCI -
Histone methyltransferase SETD2 modulates alternative splicing to inhibit intestinal tumorigenesisJCI - Histone methyltransferase SETD2 modulates alternative splicing to inhibit intestinal tumorigenesis

rMATS: robust and flexible detection of differential alternative splicing from replicate RNA-Seq data. Proc Natl Acad Sci U S A ... Alternative splicing resulting in nonsense-mediated mRNA decay: what is the meaning of nonsense? Trends Biochem Sci. 2008;33(8 ... A slow RNA polymerase II affects alternative splicing in vivo. Mol Cell. 2003;12(2):525-532.. View this article via: PubMed ... Histone methyltransferase SETD2 modulates alternative splicing to inhibit intestinal tumorigenesis. Huairui Yuan,1 Ni Li,1 Da ...
more infohttps://www.jci.org/articles/view/94292

IJMS | Free Full-Text | Linking Endoplasmic Reticular Stress and Alternative SplicingIJMS | Free Full-Text | Linking Endoplasmic Reticular Stress and Alternative Splicing

Meanwhile some early splicing changes are supplanted by new splicing changes introduced by the up-regulation of ELL2, a ... Some of the ,4000 splicing changes seen at 18 h after LPS stimulation persist into the late stages of antibody secretion, up to ... Inhibition of the mRNA-degradation function of Ire1 is correlated with further differences in the splicing patterns and a ... The mRNA-modifying function of phosphorylated Ire1 non-canonically splices Xbp1 mRNA and yet degrades other cellular mRNAs with ...
more infohttps://www.mdpi.com/1422-0067/19/12/3919
  • Recent genome-wide analyses have elucidated the extent of alternative splicing (AS) in mammals, often focusing on comparisons of splice isoforms between differentiated tissues. (nih.gov)
  • At the core of the method is the splice graph, a compact representation of a gene, its exons, introns, and alternatively spliced isoforms. (jcvi.org)
  • Using a Jurkat cell line in which expression of CD45 isoforms is sensitive to PMA stimulation, we performed a limited RNAi screen which identified HNRPLL as a major regulator of CD45 alternative splicing. (labome.org)
  • So far, the vast majority of protein-coding genes produce a single protein but there are some classic cases of alternative splicing where a given gene produces several different protein isoforms, each of which has a specific function. (blogspot.com)
  • Most of these splice variants would produce various isoforms of triose phosphate isomerase if the RNA variant were translated. (blogspot.com)
  • This gives rise to the meta-claim that almost all human genes are subject to alternative splicing and almost all human genes produce 5-10 different functional protein isoforms. (blogspot.com)
  • Just fascinating - may I ask do you think there is a spectrum with splicing errors always producing multiple isoforms but some are useful and hence can be seen by natural selection and hence selected to become more prevalent while others are detrimental and so are selected against and between these two extremes a blur of neutral or nearly isoforms which can exist to a certain extent within a tissue/cell type. (blogspot.com)
  • A key question in AD is the transition from controlled to compulsive drinking, and development of dependence may be related not only to gene expression modulated through transcriptional regulation but also through alternative splicing of genes, which may produce functionally distinct isoforms. (mdpi.com)
  • Alternative splicing results in RET isoforms with distinct trafficking properties. (biomedsearch.com)
  • RET is alternatively spliced to encode multiple isoforms that differ in their C-terminal amino acids. (biomedsearch.com)
  • The exon 4 77G allele is present at a low frequency in Caucasoids and prevents splicing from high to low molecular weight isoforms. (bl.uk)
  • The exon 6 138G allele is found at a high frequency in Far Eastern populations and promotes splicing towards low molecular weight isoforms. (bl.uk)
  • Alternative splicing - produces two protein isoforms. (academic.ru)
  • Variation of the splicing process occurs during tumor progression and may play a major role in tumorigenesis. (hindawi.com)
  • SingleSplice - detect biological variation in alternative splicing within a population of single cells. (github.com)
  • There are evolutionarily conserved features of the splicing pattern at the 5′ end of the molecule ( 27 , 29 ), thus indicating that isoform variation in TnT has deep evolutionary roots, and perhaps evolutionarily conserved functional effects. (pnas.org)
  • This approach allows us to test for associations between TnT transcript variation, muscle calcium sensitivity, and contractile performance that are independent of the developmental and physiological context in which TnT alternative splicing occurs. (pnas.org)
  • Specifically, this thesis explains how splice variation dictates the biological functions of interleukin-22 (IL-22) binding protein (IL-22BP) and interferon lambda 4 (IFNλ4), two proteins that participate in key cytokine responses to infection and inflammation. (washington.edu)
  • Using multiple promoters, when described properly, is not alternative splicing, but a transcriptional regulation mechanism. (brighthub.com)
  • However, each gene can lead to several RNA molecules through alternative splicing, an essential mechanism for multiple biological processes that can be altered in disease conditions. (eurekalert.org)
  • Thus, alternative splicing is a major gene regulatory mechanism that limits IFNλ4 bioactivity during infection, causing the genetically linked IFNλ3 to be the dominant antiviral effector instead. (washington.edu)
  • Alternative Splicing Annotation Project (ASAP) is a database for alternative splicing data. (wikipedia.org)
  • outrigger - calculate alternative splicing scores of RNA-Seq data based on junction reads and a de novo, custom annotation created with a graph database, especially made for single-cell analyses. (github.com)
  • MAASE - Convenient access, identification, and annotation of alternative splicing events (ASEs), designed specifically with experimentalists in mind. (github.com)
  • Designing effective and accurate tools for identifying the functional and structural elements in a genome remains at the frontier of genome annotation owing to incompleteness and inaccuracy of the data, limitations in the computational models, and shifting paradigms in genomics, such as alternative splicing. (jcvi.org)
  • The process is fast, accurate, and fully automated, and combines the traditionally distinct gene annotation and alternative splicing detection processes in a comprehensive and systematic way, thus considerably aiding in the ensuing manual curation efforts. (jcvi.org)
  • Mechanisms of alternative splicing are highly variable, and new examples are constantly being found, particularly through the use of high-throughput techniques. (wikipedia.org)
  • For example, although a number of alternative exons have been shown to be regulated by calcium level alterations, the underlying mechanisms are not well understood. (frontiersin.org)
  • In this communication, we will summarize the recent advances in calcium signaling-mediated alternative splicing that have provided some insights into the important regulatory mechanisms. (frontiersin.org)
  • Next, he discussed the potential mechanisms of calcium-mediated splicing control using three well-studied examples. (frontiersin.org)
  • The current review is aimed at providing an in-depth discussion of the molecular mechanisms of the dynamic control of alternative splicing regulated by calcium signaling. (frontiersin.org)
  • DESCRIPTION (provided by applicant): The long-term goal of this project is to understand the mechanisms underlying CD45 alternative splicing and the role of CD45 splicing in lymphocyte and haematopoietic cell biology. (labome.org)
  • In this review, we discuss some of the evidence suggesting that alternative splicing of candidate genes such as DRD2 (encoding dopamine D2 receptor) may form the basis of the mechanisms underlying the pathophysiology of alcoholism. (mdpi.com)
  • D ) GO analysis for significantly ( P ≤ 0.05) enriched molecular functions in validated splicing transitions of ≥20 percentage points. (nih.gov)
  • Thus, investigations of alternative splicing are essential for understanding the molecular events underlying the development of alcoholism. (mdpi.com)
  • Mechanistic characterizations indicated that SETD2 downregulation affects the alternative splicing of a subset of genes implicated in tumorigenesis. (jci.org)
  • Here we test the hypothesis that alternative splicing of TnT affects muscle calcium sensitivity and flight performance of dragonflies. (pnas.org)
  • RNA alternative splicing enables genetic efficiency and genetic diversity. (brighthub.com)
  • Alternative splicing was the first phenomenon scientists discovered that made them realize that genomic complexity cannot be judged by the number of protein-coding genes. (blogspot.com)
  • So, how do you explain the complexity of an organism with much less protein coding genes, like human genome having only 20.000 protein coding genes, in comparison to much less complex eukaryotic organisms with many more protein coding genes, if you through away the alternative splicing? (blogspot.com)
  • In this alternative splicing mode, a sequence may be simply retained or spliced out as an intron. (brighthub.com)
  • in this case, certain exons are spliced out to alter the sequence of amino acids in the expressed protein. (wikidoc.org)
  • Alternative splicing is of great importance to genetics - it invalidates the old theory of one DNA sequence coding for one polypeptide (the "one-gene-one-protein" hypothesis). (wikidoc.org)
  • Retained intron (RI): A sequence may be spliced out as an intron or retained, and there are no flanking introns. (github.com)
  • Computational analyses revealed enrichment of many sequence motifs within the upstream and downstream intronic regions near the alternatively spliced regions corresponding to binding sites of splicing regulators. (nih.gov)
  • EST pairs gapped alignment was first evaluated in Arabidopsis ( Arabidopsis thaliana ), rice ( Oryza sativa ), and tomato ( Solanum lycopersicum ) for which annotated genome sequence is available and was shown to accurately predict splicing events. (plantphysiol.org)
  • flotilla - reproduce machine learning analysis of gene expression and alternative splicing data. (github.com)
  • Are the products generated by alternative splicing functional? (nih.gov)
  • The results of the study show that alternative splicing changes lead to a general loss of functional protein domains, and particularly those domains related to functions that are also affected by genetic mutations in cancer patients. (eurekalert.org)
  • The Functional Impact of Alternative Splicing in Cancer. (eurekalert.org)
  • The CD45 gene consists of ~33 exons, of which exons 4, 5 and 6, encoding regions A, B and C of the extracellular domain respectively, can be variably spliced out. (labome.org)
  • In this application we build on our recent discovery that the heterogenous nuclear ribonucleoprotein HNRPLL is the primary regulator of CD45 alternative splicing in stimulated T cells. (labome.org)
  • We identified 95 AS events that undergo robust splicing transitions during C2C12 differentiation. (nih.gov)
  • Western analyses demonstrated that several splicing regulators undergo dynamic changes in nuclear abundance during differentiation. (nih.gov)
  • B ) The number of splicing events (out of 117 total validated events) that undergo splicing transitions of ≥20 percentage points. (nih.gov)
  • In this review, the author compiled a list of nearly 20 alternative exons that were demonstrated to undergo calcium-mediated regulation. (frontiersin.org)
  • However, regulated splicing changes are likely to be important in biological transitions such as cellular differentiation, or response to environmental stimuli. (nih.gov)
  • There are several different alternative splicing modes that occur, and there are five basic modes that are most often recognized. (brighthub.com)
  • Using data for more than 4,000 cancer patients from The Cancer Genome Atlas (TCGA project), a team led by Eduardo Eyras, ICREA research professor at the Department for Experimental and Health Sciences of the Pompeu Fabra University (DCEXS-UPF), has analyzed the changes in alternative splicing that occur in each tumor patient and studied how these changes could impact the function of genes. (eurekalert.org)
  • With this new study, we have discovered that changes in alternative splicing that occur in cancer impact protein functions in a way that is similar to that previously described for genetic mutations," he adds. (eurekalert.org)
  • This decision is made during the splicing process. (wikidoc.org)
  • An additional DNA code or other regulating process, which regulates the alternative splicing. (wikidoc.org)
  • In a new study published in the journal Cell Reports , researchers show that alterations in a process known as alternative splicing may also trigger the disease. (eurekalert.org)
  • Once researchers understand how exactly the splicing process is regulated, they may be able to predict alternative splicing products from a given gene, which will be helpful as the outcomes of RNA alternative splicing vary and include turning a gene off and changing the function of a protein. (brighthub.com)
  • SpliceR - detect alternative splicing and predict coding potential. (github.com)
  • SplitSeek - predict splice events from RNA-Seq data. (github.com)
  • The significance of the dynamic control of alternative splicing in response to changes of calcium levels has been largely unappreciated. (frontiersin.org)
  • A review published in 2008 provided a comprehensive summary of calcium-mediated splicing control ( Xie, 2008 ). (frontiersin.org)
  • MapSplice - map RNA-seq data to reference genome for splice junction discovery. (github.com)
  • More than half of the splicing transitions are conserved during differentiation of avian myoblasts, suggesting the products and timing of transitions are functionally significant. (nih.gov)