IRESite--a tool for the examination of viral and cellular internal ribosome entry sites.

Nucleic Acids Research
Martin MokrejsMartin Pospísek

Abstract

The IRESite (http://www.iresite.org) presents carefully curated experimental evidence of many eukaryotic viral and cellular internal ribosome entry site (IRES) regions. At the time of submission, IRESite stored >600 records. The IRESite gradually evolved into a robust tool providing (i) biologically meaningful information regarding the IRESs and their experimental background (including annotation of IRES secondary structures and IRES trans-acting factors) as well as (ii) thorough concluding remarks to stored database entries and regularly updated evaluation of the reported IRES function. A substantial portion of the IRESite data results purely from in-house bioinformatic analyses of currently available sequences, in silico attempts to repeat published cloning experiments, DNA sequencing and restriction endonuclease verification of received plasmid DNA. We also present a newly implemented tool for displaying RNA secondary structures and for searching through the structures currently stored in the database. The supplementary material contains an updated list of reported IRESs.

References

Dec 31, 2005·Nucleic Acids Research·Martin MokrejsMartin Pospísek
Sep 8, 2006·RNA·Stephen D BairdMartin Holcik
Oct 20, 2006·IEEE/ACM Transactions on Computational Biology and Bioinformatics·Matthias HöchsmannRobert Giegerich
Feb 13, 2007·Free Radical Biology & Medicine·Isabella SaviniLuciana Avigliano
Jun 27, 2007·Nucleic Acids Research·Stephen D BairdMartin Holcik
Mar 11, 2008·Proceedings of the National Academy of Sciences of the United States of America·Brian T BaranickChristopher R Logg
Apr 19, 2008·Trends in Microbiology·Encarnación Martínez-Salas
Oct 23, 2008·Nucleic Acids Research·Eric W SayersJian Ye
Oct 23, 2008·Nucleic Acids Research·Dennis A BensonEric W Sayers
Oct 28, 2008·Nucleic Acids Research·Paul P GardnerAlex Bateman
Apr 29, 2009·Bioinformatics·Kévin DartyYann Ponty
May 15, 2009·Biochimica Et Biophysica Acta·Michael Niepmann
Jul 28, 2009·Biochimica Et Biophysica Acta·Laurent BalvayThéophile Ohlmann

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Citations

May 4, 2012·Nature·Carson C ThoreenDavid M Sabatini
Jun 19, 2013·Nature Methods·Brian P WellensiekJohn C Chaput
Jan 5, 2011·Nucleic Acids Research·Michael Y Galperin, Guy R Cochrane
Dec 7, 2011·Nucleic Acids Research·Michael Y Galperin, Xosé M Fernández-Suárez
Mar 1, 2012·Nucleic Acids Research·Sita J LangeRolf Backofen
Feb 14, 2012·Journal of Cell Science·Scott B FergusonTrudi Schüpbach
Jul 19, 2014·Plasmid·Maysam Mansouri, Philipp Berger
Mar 21, 2013·Nature Communications·Julien PérardMarc Jamin
Dec 25, 2015·Biochimie·Victoria V SmirnovaIvan N Shatsky
Feb 6, 2013·Therapeutic Apheresis and Dialysis : Official Peer-reviewed Journal of the International Society for Apheresis, the Japanese Society for Apheresis, the Japanese Society for Dialysis Therapy·Theodoros EleftheriadisIoannis Stefanidis
Jan 5, 2012·Wiley Interdisciplinary Reviews. RNA·Terra-Dawn M Plank, Jeffrey S Kieft
Oct 16, 2015·Nucleic Acids Research·Sai ZhangJianyang Zeng
Nov 10, 2012·Nucleus·Jennifer L Gerton
Jan 12, 2011·Cell Cycle·Anton A Komar, Maria Hatzoglou
Jan 27, 2015·ELife·Dmitry E AndreevPavel V Baranov
Nov 20, 2014·Nature·Jonathan D Dinman
Jun 15, 2016·Biochemistry. Biokhimii︠a︡·E S MardanovaN V Ravin
Jun 7, 2016·Scientific Reports·Pandurang KolekarAbhijeet Kulkarni
Mar 6, 2016·Journal of Medical Genetics·Yonghua ChenXubao Liu
Jul 28, 2016·Biochimica Et Biophysica Acta·Javier T Granados-Riveron, Guillermo Aquino-Jarquin
Jul 22, 2016·RNA Biology·Shira Weingarten-Gabbay, Eran Segal
Aug 26, 2016·Journal of Molecular Medicine : Official Organ of the Gesellschaft Deutscher Naturforscher Und Ärzte·Elena AndreucciLucia Magnelli
Sep 21, 2016·Biochemical and Biophysical Research Communications·Florence Bonnet-MagnavalEric Lacazette
Jan 25, 2017·Nucleic Acids Research·Guozhen GaoMark T Bedford
Feb 28, 2017·PLoS Genetics·Hyun Yong JinChangchun Xiao
Jan 20, 2018·International Journal of Genomics·Luka BolhaDamjan Glavač
Sep 19, 2017·PLoS Computational Biology·Alexey A GritsenkoEran Segal
May 12, 2012·Nature·Dan DominissiniGideon Rechavi
Nov 23, 2017·Nature Reviews. Molecular Cell Biology·Kathrin LeppekMaria Barna
Sep 11, 2019·Journal of Molecular Cell Biology·Yun Yang, Zefeng Wang
Jan 8, 2020·BioEssays : News and Reviews in Molecular, Cellular and Developmental Biology·Lei-Yun WangJi-Ye Yin
Jan 31, 2020·Briefings in Bioinformatics·Marieke VrommanPieter-Jan Volders

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Datasets Mentioned

BETA
EU919738
EU919739

Methods Mentioned

BETA
PCR
gypsy

Software Mentioned

align
BLAST
RNAforester
VARNA
IRESite

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