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Protocols

IRESite specifications

Information


Unique identifier OMICS_10065
Name IRESite
Restrictions to use None
Maintained Yes

Maintainer


  • person_outline TIRESite Team

Publications for IRESite

IRESite citations

 (5)
library_books

First Evidence for Internal Ribosomal Entry Sites in Diverse Fungal Virus Genomes

2018
MBio
PMCID: 5874917
PMID: 29559577
DOI: 10.1128/mBio.02350-17

[…] e detection of IRESs or similar translational regulatory elements had been developed in filamentous fungi until recently (, ). There are online IRES prediction tools available, like Pfam 12.0 (http://iresite.org/) () and IRESPred (http://bioinfo.net.in/IRESPred/) (). Nevertheless, because of the lack of sequence and structural similarity conserved across different types of IRESs, it is difficult t […]

library_books

Know Your Enemy: Successful Bioinformatic Approaches to Predict Functional RNA Structures in Viral RNAs

2018
Front Microbiol
PMCID: 5758548
PMID: 29354101
DOI: 10.3389/fmicb.2017.02582

[…] g particular structural or functional classes of elements, some of which are overrepresented in viruses. The database of pseudoknots (Pseudobase++) contains 252 virus records (accessed in June 2017). IRESite contains 44 viral IRES entries (June 2017; Mokrejs et al., ). Recode contains many viral recoding sites, in particular RNA elements stimulating frameshifting and readthrough (Bekaert et al., ) […]

library_books

Circular RNAs: Biogenesis, Function, and a Role as Possible Cancer Biomarkers

2017
Int J Genomics
PMCID: 5733622
PMID: 29349062
DOI: 10.1155/2017/6218353

[…] Splice, and segemehl utilize the fragmented-based approach. In addition, several integrated tools aimed to identify circRNAs with a protein-coding potential have been developed, including CircPro [], IRESite [], CPAT [], Pfam 31.0 [], PhyloCSF [], and ORF Finder from the NCBI database. Also, the TopHat-Fusion algorithm has been designed to detect circRNAs that are derived from gene fusion events [ […]

call_split

A Novel Method for Gene Specific Enhancement of Protein Translation by Targeting 5’UTRs of Selected Tumor Suppressors

2016
PLoS One
PMCID: 4865139
PMID: 27171412
DOI: 10.1371/journal.pone.0155359
call_split See protocol

[…] Total Gibbs energy prediction (ΔG = ΔH—TΔS) of 5’UTR secondary structures was performed using RNAstructure version 5.2 []. NCBI-BLASTN program and IRESite database [] were used for comparative sequence analysis towards evolutionary conserved 5’UTR domains such as IRES consensus sequences. The dGenhancer calculator was used to determine translati […]

library_books

Translation of 5′ leaders is pervasive in genes resistant to eIF2 repression

2015
eLife
PMCID: 4383229
PMID: 25621764
DOI: 10.7554/eLife.03971.021

[…] ference in ribosome footprint density was divided by the CDS length to prevent skewing of results in favour of transcripts with longer coding regions.The list of human cellular IRES was obtained from IRESite () on 2 August 2014.We identified the most probable translation initiation sites by manually examining the ribo-seq profiles of eight translationally resistant genes (PPP1R15A, IFRD1, SLC35A4, […]


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IRESite institution(s)
Charles University, Faculty of Science, Department of Genetics and Microbiology Vinicna 5, Prague, Czech Republic
IRESite funding source(s)
Ministry of Education Youth and Sports of the Czech Republic (grant numbers LC06066, MSM0021620813, MSM0021620858 and 1M06014); Czech Science Foundation (grant number 301/07/0607)

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