5,380 Hits in 6.3 sec

A General Definition and Nomenclature for Alternative Splicing Events

Michael Sammeth, Sylvain Foissac, Roderic Guigó, Michael R. Brent
2008 PLoS Computational Biology  
In this work, we present a general definition of the AS event along with a notation system that involves the relative positions of the splice sites.  ...  This nomenclature univocally and dynamically assigns a specific "AS code" to every possible pattern of splicing variation.  ...  Denoeud and J. Mudge of the HAVANA annotation team for sharing their expertise on Gencode, as well as T. Alioto, A. Kedzierska, T. Kisiel, H. Tilgner, V. Lacroix, J. Lagarde, and O.  ... 
doi:10.1371/journal.pcbi.1000147 pmid:18688268 pmcid:PMC2467475 fatcat:zsgljanskjet5k62kp2wwg4wma

A survey of alternative transcripts of human tissue kallikrein genes

Lisa Kurlender, Carla Borgono, Iacovos P. Michael, Christina Obiezu, Marc B. Elliott, George M. Yousef, Eleftherios P. Diamandis
2005 Biochimica et Biophysica Acta. CR. Reviews on Cancer  
The most common alternative splicing event is exon skipping (35%) and the least common events are cryptic exons (3%) and internal exon deletion (3%).  ...  In the kallikrein locus, the majority of alternative splicing events occur within the protein-coding region, and to a lesser extent in the 5V untranslated regions (UTRs).  ...  For more details, see legend of Fig. 4 Table 1 1 Nomenclature and schematic representation of splicing events Our definition Definition by Wang et al. [17] Schematic representation Skipped exon  ... 
doi:10.1016/j.bbcan.2005.02.001 pmid:15878240 fatcat:5evb6uah4vbybnkt57gq3mhnma

ASTALAVISTA: dynamic and flexible analysis of alternative splicing events in custom gene datasets

S. Foissac, M. Sammeth
2007 Nucleic Acids Research  
In the process of establishing more and more complete annotations of eukaryotic genomes, a constantly growing number of alternative splicing (AS) events has been reported over the last decade.  ...  ASTALAVISTA (alternative splicing transcriptional landscape visualization tool) employs an intuitive and complete notation system to univocally identify such events.  ...  Eyras and other members of the PRBB for inspiring and fruitful discussions. This work has been supported by a post-doctoral fellowship to M.S.  ... 
doi:10.1093/nar/gkm311 pmid:17485470 pmcid:PMC1933205 fatcat:e3mjvnu6qfeavmxksstkra6wn4

Corepressors: custom tailoring and alterations while you wait

Michael Goodson
2005 Nuclear Receptor Signaling  
It is now clear that the functions of both SMRT and N-CoR are further diversified through alternative mRNA splicing, yielding a series of corepressor protein variants that participate in distinctive transcription  ...  factor partnerships and display distinguishable repression properties.This review will discuss what is known about the structure and actions of SMRT, N-CoR, and their splicing variants, and how alternative  ...  Acknowledgements The research attributed to our laboratory was supported by the Public Health Service/National Institutes of Health through awards R37CA53394 (MLP), RO1DK53538 (MLP), 5F32DK062654 (MG), and  ... 
doi:10.1621/nrs.03003 pmid:16604171 pmcid:PMC1402215 fatcat:524njiubt5evxkpjtinsp5eljq

PrimerSeq: Design and Visualization of RT-PCR Primers for Alternative Splicing Using RNA-seq Data

Collin Tokheim, Juw Won Park, Yi Xing
2014 Genomics, Proteomics & Bioinformatics  
The vast majority of multi-exon genes in higher eukaryotes are alternatively spliced and changes in alternative splicing (AS) can impact gene function or cause disease.  ...  We have developed PrimerSeq, a user-friendly software for systematic design and visualization of RT-PCR primers using RNA-seq data.  ...  We thank Zhixiang Lu for testing PrimerSeq and performing RT-PCR experiments.  ... 
doi:10.1016/j.gpb.2014.04.001 pmid:24747190 pmcid:PMC4411361 fatcat:oqtcjfiupnb4bj46rgo23dpdgy

SplAdder: Identification, quantification and testing of alternative splicing events from RNA-Seq data [article]

Andre Kahles, Cheng Soon Ong, Yi Zhong, Gunnar Rätsch
2015 bioRxiv   pre-print
Whereas an identification of complete transcripts is technically challenging and computationally expensive, focusing on single splicing events as a proxy for transcriptome characteristics is fruitful and  ...  splicing events present in the augmented annotation graph, iii) quantify and confirm these events based on the RNA-Seq data, and iv) test for significant quantitative differences between samples.  ...  Acknowledgements The authors are grateful to Vipin T Sreedharan for providing code to convert annotation files, to Andreas Wachter for valuable discussions and feedback on the software and to David Kuo  ... 
doi:10.1101/017095 fatcat:a2bggwnlwvhmldf2reemx5gc6u

CD44 glycoprotein in cancer: a molecular conundrum hampering clinical applications

Rita Azevedo, Cristiana Gaiteiro, Andreia Peixoto, Marta Relvas-Santos, Luís Lima, Lúcio Lara Santos, José Alexandre Ferreira
2018 Clinical Proteomics  
However, CD44 is a general designation for a large family of splicing variants exhibiting different degrees of glycosylation and, potentially, functionally distinct roles.  ...  Herein, we attempt to comprehensively address these aspects and systematize CD44 nomenclature, setting milestones for biomarker discovery.  ...  Availability of data and materials Data sharing not applicable to this article as no datasets were generated or analysed during the current study.  ... 
doi:10.1186/s12014-018-9198-9 pmid:29983670 pmcid:PMC6020424 fatcat:ulgzkz3hbzhclfjco3sspfv6oa

Current Challenges in Studying Alternative Splicing in Plants: The Case of Physcomitrella patens SR Proteins

José Pedro Melo, Maria Kalyna, Paula Duque
2020 Frontiers in Plant Science  
Despite being well studied in animals and a few plant species, such as the model angiosperm Arabidopsis thaliana and the crop Oryza sativa, little is known of these splicing factors in early land plants  ...  Alternative splicing - an RNA processing mechanism through which splice sites are differentially recognized, originating multiple transcripts and potentially different proteins from the same gene - can  ...  2010) , who proposed a standardization of the definition and nomenclature of SR proteins.  ... 
doi:10.3389/fpls.2020.00286 pmid:32265953 pmcid:PMC7105729 fatcat:juuru4csunhrdf3mjb5u6clcn4

The dynamic landscape of fission yeast meiosis alternative-splice isoforms

Zheng Kuang, Jef D. Boeke, Stefan Canzar
2016 Genome Research  
We reveal 17017 alternative splicing events in 19741 novel isoforms at different stages of meiosis, including antisense and read-through transcripts.  ...  Alternative splicing increases the diversity of transcriptomes and proteomes in metazoans.  ...  Acknowledgements We thank Haiping Hao for assistance with sequencing, and Alix Kieu and Roberto LIeras, Pacific Biosystems, for in kind contribution of SMRT cells and suggestions for analysis.  ... 
doi:10.1101/gr.208041.116 pmid:27856494 pmcid:PMC5204338 fatcat:w7zlx6dg6jgl3mmhcixwwm356e

The dynamic landscape of fission yeast meiosis alternative-splice isoforms [article]

Zheng Kuang, Jef D. Boeke, Stefan Canzar
2016 bioRxiv   pre-print
We reveal 17017 alternative splicing events in 19741 novel isoforms at different stages of meiosis, including antisense and read-through transcripts.  ...  Alternative splicing increases the diversity of transcriptomes and proteomes in metazoans.  ...  Acknowledgements We thank Haiping Hao for assistance with sequencing, and Alix Kieu and Roberto LIeras, Pacific Biosystems, for in kind contribution of SMRT cells and suggestions for analysis.  ... 
doi:10.1101/045922 fatcat:nne7rcfnrjfu7fcqzbtuyqyeqi

Complete Alternative Splicing Events Are Bubbles in Splicing Graphs

Michael Sammeth
2009 Journal of Computational Biology  
Eukaryotic splicing structures are known to involve a high degree of alternative forms derived from a premature transcript by alternative splicing (AS).  ...  Key words alternative splicing, alternative splicing event, complete event, ESTs, splicing graph, history of alternative splicing, mutually exclusive exons, double exon skipping 2  ...  Then firstly I give a general definition of AS events that involve two or more alternatives (Section 2.1) and the terminology subsequently used for describing them, including a nomenclature to name their  ... 
doi:10.1089/cmb.2009.0108 pmid:19689216 fatcat:lxblshd7tvcc3gmdyhm6lw6mpm

DBASS3 and DBASS5: databases of aberrant 3'- and 5'-splice sites

E. Buratti, M. Chivers, G. Hwang, I. Vorechovsky
2010 Nucleic Acids Research  
Finally, this resource will be useful for fine-tuning splice-site prediction algorithms, better definition of auxiliary splicing signals and design of new reporter assays.  ...  DBASS3 and DBASS5 currently contain approximately 900 records of cryptic and de novo 3 0 -and 5 0 -splice sites that were produced by over a thousand different mutations in approximately 360 genes.  ...  and see for other genes) give a list of splicing mutations.  ... 
doi:10.1093/nar/gkq887 pmid:20929868 pmcid:PMC3013770 fatcat:2yvz57xgdnad5mor2qemyu3cwi

Detecting splicing patterns in genes involved in hereditary breast and ovarian cancer

Grégoire Davy, Antoine Rousselin, Nicolas Goardon, Laurent Castéra, Valentin Harter, Angelina Legros, Etienne Muller, Robin Fouillet, Baptiste Brault, Anna S Smirnova, Fréderic Lemoine, Pierre de la Grange (+10 others)
2017 European Journal of Human Genetics  
Here we present a custom RNA-Seq assay plus bioinformatics and biostatistics pipeline to analyse specifically alternative and abnormal splicing junctions in 11 targeted HBOC genes.  ...  Our pipeline identified 14 new alternative splices in BRCA1 and BRCA2 in addition to detecting the majority of known alternative spliced transcripts therein.  ...  We thank the Brazilian agency Conselho Nacional de Desenvolvimento Científico e Tecnológico (CNPq) for providing a postdoctoral fellowship for ASS.  ... 
doi:10.1038/ejhg.2017.116 pmid:28905878 fatcat:3v4t6o7inzccpavi6ijr23nega

Spliceosome twin introns in fungal nuclear transcripts

Michel Flipphi, Erzsébet Fekete, Norbert Ág, Claudio Scazzocchio, Levente Karaffa
2013 Fungal Genetics and Biology  
GU doublet functioning as 384 the donor site for this ''internal intron'' and that the excision of 385 the internal intron generates a new canonical donor site leading 386 to a second splicing event which  ...  (Panel A) Hypothetical [D4.5] stwintron as predicted for this gene. Nomenclature as in Figs. 2 and 3.  ... 
doi:10.1016/j.fgb.2013.06.003 pmid:23792080 fatcat:ti3cfvxu3je3td6gz4uesoch5e

Studies of alternative isoforms provide insight into TDP-43 autoregulation and pathogenesis

S. D'Alton, M. Altshuler, J. Lewis
2015 RNA: A publication of the RNA Society  
We detail the existence of a plethora of complex splicing events and alternative poly(A) use and provide data that explain the discrepancies reported to date regarding the autoregulatory capacity of TDP  ...  Finally, we use a novel cytoplasmic isoform of TDP to induce disease-like loss of soluble, nuclear TDP-43, which results in aberrant splicing and up-regulation of endogenous TARDBP.  ...  A second group confirmed the splicing event in the 3 ′ UTR and additionally demonstrated that this event is coupled to use of an alternative polyadenylation site, but found no evidence for up-regulation  ... 
doi:10.1261/rna.047647.114 pmid:26089325 pmcid:PMC4509932 fatcat:cf5u3agcxjezvolm6rihlhzl5i
« Previous Showing results 1 — 15 out of 5,380 results