• Alternative splicing of pre-mRNA is a post-transcriptional modification essential for the regulation of gene expression and function. (biomedcentral.com)
  • Through alternative splicing, multiple transcripts are produced from a single mRNA precursor, widely expanding proteome diversity. (biomedcentral.com)
  • We previously found that this interference affected the activity of splice regulatory proteins and a T cell inhibitory protein isoform was produced from an alternatively spliced pre-mRNA. (uni-wuerzburg.de)
  • The hnRNP complex is involved in pre-mRNA splicing and the export of fully processed mRNA to the cytoplasm. (origene.com)
  • Homo sapiens Fc fragment of IgG receptor IIa (FCGR2A), transcript variant 2, mRNA. (origene.com)
  • These data place Pnn at the fulcrum point between chromatin and mRNA splicing. (molvis.org)
  • Mus musculus apolipoprotein D (Apod), transcript variant 3, mRNA. (genscript.com)
  • Homo sapiens potassium voltage-gated channel subfamily A regulatory beta subunit 2 (KCNAB2), transcript variant 2, mRNA. (ucsc.edu)
  • Several variants of the receptor exist due to multiple ALTERNATIVE SPLICING of its mRNA. (bvsalud.org)
  • This includes variants in sequences that regulate messenger RNA (mRNA) splicing and synonymous variants that lead to a change between two codons for the same amino acid, thereby not directly altering the protein-coding sequence. (lu.se)
  • Synonymous variants can still be functional, e.g. through effects on mRNA splicing and stability, as well as the speed of translation and protein folding. (lu.se)
  • However, although many thousands of alternatively spliced transcripts are routinely detected in RNA-seq studies, reliable large-scale mass spectrometry-based proteomics analyses identify only a small fraction of annotated alternative isoforms. (blogspot.com)
  • To further investigate PNN's role in regulating the alternative splicing of lncRNAs in a corneal epithelial context, we performed detailed analyses for detecting and identifying alternatively spliced lncRNAs. (molvis.org)
  • Methods: Total RNA was isolated from PNN knockdown human corneal epithelial (HCET) cells or Pnn-deficient mouse corneas, and subjected to real-time-PCR (RT-PCR) assays, and the alternatively spliced lncRNAs were counted. (molvis.org)
  • Alternatively spliced lncRNAs were detected with in situ hybridization with variant-specific RNA probes on human cornea sections. (molvis.org)
  • The performance of this splice array was validated with artificial constructs for CDC6 , VEGF , and PCBP4 isoforms. (biomedcentral.com)
  • None of these splicing isoforms had been previously associated with lung cancer. (biomedcentral.com)
  • In recent years, powerful techniques for genome-wide identification and analysis of alternative splicing isoforms have been developed. (biomedcentral.com)
  • Proponents of massive alternative splicing argue that most human genes produce many different protein isoforms. (blogspot.com)
  • Opponents (I am one) argue that most splice variants are due to splicing errors and most of those predicted protein isoforms don't exist. (blogspot.com)
  • The clearest finding from proteomics experiments is that most human genes have a single main protein isoform, while those alternative isoforms that are identified tend to be the most biologically plausible: those with the most cross-species conservation and those that do not compromise functional domains. (blogspot.com)
  • However, large-scale proteomics experiments identify few alternative isoforms. (blogspot.com)
  • While a small number of alternative isoforms are conserved across species, have strong tissue dependence, and are translated in detectable quantities, most have variable tissue specificities and appear to be evolving neutrally. (blogspot.com)
  • My colleague at the University of Toronto, Ben Blencowe, is a strong supporter of alternative splicing and its role in creating multiple isoforms of most proteins. (blogspot.com)
  • Alternative splicing of this gene results in multiple transcript variants encoding distinct isoforms. (ucsc.edu)
  • There are multiple isoforms of each of these proteins, either encoded by different genes or the result of alternative splicing of transcripts. (thermofisher.com)
  • Alternative splicing occurs at this locus and two variants, each encoding distinct isoforms, are described. (novusbio.com)
  • A large-scale sequencing screen of X-linked synaptic genes in individuals with autism spectrum disorder (ASD) or schizophrenia (SCZ), two common neurodevelopmental disorders, identified many variants most of which have no easily predictable effect on gene function. (nih.gov)
  • We developed a simple algorithm based on a splicing index to detect genes that undergo alternative splicing (AS) or are differentially regulated (RG) upon T cell suppression. (uni-wuerzburg.de)
  • Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway analyses were performed to explore the function of splicing factors (SFs) that were associated with AS events. (frontiersin.org)
  • Whole-genome assemblies of wild Oryza species will provide new sources of genes and gene variants/haplotypes, enhancing the ability of breeding programs to introduce desirable traits into domestic cultivars. (nature.com)
  • Especially in familial breast cancer we believe that the chances of finding previously overlooked variants in known high-risk genes are higher than to find new, rare risk loci. (lu.se)
  • Variants in blood pressure genes and the risk of Accardi R, Rubino R, Scalise M et col . (2011). (who.int)
  • Hypothesis Differentially regulated and alternatively splice variant transcripts accumulating in response to PI3K abrogation in T cells potentially encode proteins involved in T cell silencing. (uni-wuerzburg.de)
  • Indeed, most alternative exons do not seem to be under selective pressure, suggesting that a large majority of predicted alternative transcripts may not even be translated into proteins. (blogspot.com)
  • Alternative splicing of gene can generate multiple transcripts and proteins to regulate tissue and organ development [ 17 ]. (hindawi.com)
  • The hypoxia-regulated alternative TrkAIII splice variant expressed by human neuroblastomas exhibits oncogenic potential, driven by in-frame exon 6 and 7 alternative splicing, leading to omission of the receptor extracellular immunoglobulin C(1) domain and several N-glycosylation sites. (cnr.it)
  • In proband 1 (V1/V2), V1 was predicted to introduce a premature termination codon (PTC), whereas V2 disrupted the exon 41 splice donor site causing incomplete skipping of exon 41. (nature.com)
  • As the common IRD variants have largely been identified, exome sequencing or genome sequencing identify rare variants that require functional validation. (nature.com)
  • However, since they are not specifically designed to examine alternative splicing, they fail to detect events such as the alternative use of 5' or 3' splice sites, intron retention, or the insertion of cryptic exons. (biomedcentral.com)
  • Our main aims are to 1) provide a detailed understanding of how variants in regulatory motifs control alternative splicing and intron retention, and 2) develop accurate methods for identification of functional synonymous variants. (lu.se)
  • Comparing to microarray, sequencing-based RNA-seq is able to identify splicing variants and single nucleotide variants in one experiment simultaneously. (nih.gov)
  • We have developed PVAAS, a tool to identify single nucleotide variants that associated with aberrant alternative splicing from RNA-seq data. (nih.gov)
  • The controversy can only be resolved when proponents of massive alternative splicing provide evidence to support their claim that there are 100,000 functional proteins. (blogspot.com)
  • I think the term "alternative splicing" should be restricted to genuine examples of real alternative slicing that generate different functional proteins. (blogspot.com)
  • This suggests that most annotated alternative variants are unlikely to have a functional cellular role as proteins. (blogspot.com)
  • However, the transcript variant and temporal expression pattern of EZH2 in the middle and late porcine fetus are still unknown. (hindawi.com)
  • In this study, we identified a transcript variant of EZH2 in porcine fetal tissues by cloning and sequencing. (hindawi.com)
  • The enormous variants and mutations found mean that we are still far from being able to concretely clarify a genotype-phenotype relationship. (bvsalud.org)
  • Based on the TBX5, GATA4, and HEY2, often simultaneously incidence of somatic mutations described in the within the same patient.9-13 The observation of two previously published reports, our study was adequately or more somatic sequence variants in the same powered to replicate the previous studies. (cdc.gov)
  • 3 When no pathogenic variant is identified, exome sequencing or genome sequencing may help uncover the variants missed by panel-based screening. (nature.com)
  • Microarrays strategies, which allow for the characterization of thousands of alternative splice forms in a single test, can be applied to identify differential alternative splicing events. (biomedcentral.com)
  • The platform was then applied to the analysis of differential splice forms in lung cancer samples compared to matched normal lung tissue. (biomedcentral.com)
  • These large-scale high-throughput analytical methods have been applied to the identification of differential splicing events in cancer tissues [ 8 ]. (biomedcentral.com)
  • The use of splice-junction oligonucleotides to analyze splice events was proposed as early as 1986, when Morgan and Ward used them to identify differential splice forms of minute virus in mice cDNA [ 14 ]. (biomedcentral.com)
  • Conclusions PI3K abrogation interferes with key T cell activation processes through both differential expression and alternative splicing, which together actively contribute to T cell suppression. (uni-wuerzburg.de)
  • Interestingly, a mouse ortholog of HAS2-AS1, Has2as, clearly exhibited a differential splicing pattern among three major splice variants in the Pnn-deficient mouse cornea. (molvis.org)
  • Knockdown of PNN in HCET cells led to specific changes in the inclusion of multiple cassette exons as well as in the use of alternative splice sites in RP11-322M19.1 and RP11-18I14.1, resulting in considerable net changes in the ratio between the splice variants. (molvis.org)
  • Our goal was to identify the variants which might either create or disrupt an acceptor splice site, a donor splice site or an exonic splicing enhancer, thus leading to aberrant splicing that could be involved in the pathogenesis of ASD or SCZ. (nih.gov)
  • This provides unique opportunity to detect variants that associated with aberrant splicing. (nih.gov)
  • Despite the popularity of RNA-seq, no bioinformatics tool has been developed to leverage this advantage to identify variants associated with aberrant splicing. (nih.gov)
  • iii) assess the significance of association between variants and aberrant splicing events. (nih.gov)
  • In vitro assays were developed to validate the variants identified (fibroblast assay, induced pluripotent stem cell [iPSC] derived retinal organoids, and a dynein motility assay). (nature.com)
  • Alternative splicing is well documented at the transcript level, and microarray and RNA-seq experiments routinely detect evidence for many thousands of splice variants. (blogspot.com)
  • The sequence analyses and quantification of splice variants of candidate lncRNAs, including RP11-295B20.2, RP11-18I14.1, and RP11-322M19.1, demonstrated complex configuration of their splicing changes, with a significant impact of PNN on the process. (molvis.org)
  • The algorithm used to distinguish changes in expression from changes in splicing was calibrated using internal non-spliced control sequences. (biomedcentral.com)
  • Purpose: GG-H whole transcriptome array analysis suggested involvement of PININ (PNN) in the alternative splicing of multiple long non-coding RNAs (lncRNAs). (molvis.org)
  • The purpose of this project is to understand how specific types of genetic variants, which traditionally have not been extensively studied, can affect breast cancer risk and tumour characteristics through effects on the transcriptome and proteome. (lu.se)
  • Alternative splicing results in multiple variants. (wikipedia.org)
  • Results: One non-synonymous germline sequence variant iants as well as multiple haplotypes were observed was identified in one patient. (cdc.gov)
  • The gap between the numbers of alternative variants detected in large-scale transcriptomics experiments and proteomics analyses is real and is difficult to explain away as a purely technical phenomenon. (blogspot.com)
  • While alternative splicing clearly does contribute to the cellular proteome, the proteomics evidence indicates that it is not as widespread a phenomenon as suggested by transcript data. (blogspot.com)
  • In particular, the popular view that alternative splicing can somehow compensate for the perceived lack of complexity in the human proteome is manifestly wrong . (blogspot.com)
  • In this report, we evaluated the impact of these rare missense and silent variants on gene splicing. (nih.gov)
  • Furthermore, missense and silent variants in nuclear RNA export factor 5 and histone deacetylase 6 were shown to partially disrupt the protein. (nih.gov)
  • Lamin A/C cumulative protein expression of all variants is reported by semi-quantitative Western blotting. (mdpi.com)
  • Role of common and rare APP DNA sequence variants in Alzheimer disease. (cdc.gov)
  • Dr Michael Mitchell, Division of Cardiothoracic Surgery, defects (ASD, n = 13), ventricular septal defects (VSD, NKX2-5 sequence variants were found in .95% of Department of Surgery, Medical n = 5), and atrioventricular canal defects (AVCD, n = 10). (cdc.gov)
  • Accepted 1 August 2008 the same methodology described in the previously that somatic sequence variants occur with high published reports. (cdc.gov)
  • Two synonymous germline in a majority of these patients.10 13 The same sequence variants were identified in two separate investigators also found somatic sequence variants patients. (cdc.gov)
  • The somatic NKX2-5 sequence variants were defects. (cdc.gov)
  • To date, a lot of EZH2 variants have been found in various cell and tissue types [ 18 - 20 ]. (hindawi.com)
  • Tumor-specific variations in splicing may generate new epitopes that can serve as a starting point for immune therapy or targeted delivery, as well as for the development of new diagnostic or prognostic tools [ 6 ]. (biomedcentral.com)
  • Note: I strongly object to using "alternative splicing" as a synonym for "detection of large numbers of splice variants. (blogspot.com)
  • For example, cancer-related aberrantly spliced variants have been shown to be actively involved in the initiation and/or progression of some types of cancer [ 4 ]. (biomedcentral.com)
  • Considering the varieties of EZH2 splicing variant, identifying its transcript in porcine fetal tissues is the foundation to study its function. (hindawi.com)
  • Moreover, none of the EZH2 transcript variants have yet been identified in porcine fetal tissues. (hindawi.com)
  • However, only one transcript has been validated in pigs, with several other transcript variants of EZH2 from digital computational analysis in NCBI that have not been empirically validated. (hindawi.com)
  • A rare loss-of-function variant of ADAM17 is associated with late-onset familial Alzheimer disease. (cdc.gov)
  • Biallelic variants in the cilia gene DYNC2H1 have been associated with two severe ciliopathies: Jeune asphyxiating thoracic dystrophy (JATD, MIM 613091) and short-rib polydactyly (SRP, MIM 613091) with only four documented cases of associated complex early retinal degeneration at ages 2 months, and 2, 5, and 11 years old. (nature.com)
  • Conclusions: The data suggest PNN's role in the alternative splicing of a specific subset of lncRNAs might have a significant impact on the corneal epithelium. (molvis.org)
  • Determining the role of DYNC2H1 variants in nonsyndromic inherited retinal disease (IRD). (nature.com)