UTRScan protocols

View UTRScan computational protocol

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UTRScan specifications

Information


Unique identifier OMICS_24951
Name UTRScan
Interface Web user interface
Restrictions to use None
Input data A sequence.
Input format FASTA
Programming languages Perl
Computer skills Basic
Stability Stable
Maintained Yes

Maintainer


  • person_outline Graziano Pesole <>

Publications for UTRScan

UTRScan in pipelines

 (4)
2013
PMCID: 3747860
PMID: 23676078
DOI: 10.1186/1471-2164-14-331

[…] used. a script (‘domain_compare.py’) was used to identify if domains were retained, lost or gained relative to the closest matching transcript. detection of motifs in the 3’utr was performed using utrscan []., we used astalavista version 2.2 [] to quantify alternative splicing events. this program takes as input a gtf file (fpkm > 3) and outputs all splicing events in the annotation […]

2012
PMCID: 3582483
PMID: 23127152
DOI: 10.1186/1471-2164-13-595

[…] to identify evolutionarily conserved regulatory motifs in catfish transcripts, we searched the utr database collection (utrdb) [] using the 5’ and 3’ utrs as queries with the pattern match program utrscan., the authors declare that they have no competing interests., sl conducted the major part of the research including preparation of the samples, bioinformatic analysis and manuscript […]

2010
PMCID: 2902525
PMID: 20634964
DOI: 10.1371/journal.pone.0011546

[…] l = 6, w = 6., to search conserved candidate regulatory motifs in catfish transcripts, all 5′ and 3′ utrs were used as queries to search against the utrdb by using pattern matcher program utrscan., all channel catfish and blue catfish full-length cdna sequences were used to conduct blastx searches against the uniprot database. sequences that shared the same top blastx hit […]

2010
PMCID: 3017843
PMID: 21083898
DOI: 10.1186/1471-2229-10-251

[…] extracted to excel sheets. different structural components namely, coding and untranslated regions (5'utrs and 3'utrs) in the unigene sequences was determined using the software tools fgenesh [] and utrscan [], respectively. the aminoacid sequences encoded by the predicted coding nucleotide regions of the microsatellite carrying unigenes were analyzed using the software pfam [] to determine […]


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UTRScan in publications

 (53)
PMCID: 5854547
DOI: 10.1016/j.omtn.2018.01.011

[…] introduces a number of new regulatory mechanisms into the transcript that negatively impact on protein expression., in silico analysis of the extended 3′ utr was carried out using the online tools utrscan, mirbase, polyadq, and dna functional site miner (dna fs miner). lists the potential regulatory elements identified within intron 7 from each of these databases, and a illustrates […]

PMCID: 5601403
PMID: 28955198
DOI: 10.3389/fnmol.2017.00279

[…] apa events in both the ellis and voineagu datasets was used in a series of searches for regulatory elements. the rbpmap () web server was used to find rna-binding protein target motifs. the utrscan () tool was used to find utr elements. finally, mirna binding sites were retrieved from the results of targetscan () available from the ucsc genome browser ()., lists of synaptic […]

PMCID: 5496269
PMID: 28676128
DOI: 10.1186/s13023-017-0678-1

[…] were performed by swiss pdb viewer, which revealed specific structural changes responsible for the functional impacts of these snps. additionally, snps in the untranslated region were analyzed by utrscan and polymirts. moreover, by investigating known pathogenic mutations and relevant patient phenotypes in previous publications, phenotype severity (severe, intermediate or mild) […]

PMCID: 5343461
PMID: 28276452
DOI: 10.1038/srep43861

[…] translation of downstream protein coding regions of a gene. therefore, the 5′ utrs of the genes in the set of translationally regulated genes were searched for open reading frames (orfs) using the utrscan program, which finds matches to experimentally verified or predicted uorfs from literature (see pesole, g., et al.). the results show that approximately 19% (89/455) of the genes contain one […]

PMCID: 5363706
PMID: 28272408
DOI: 10.1038/srep43830

[…] polymorphism (snp). in silico analysis of 95 missense snp’s corresponding to the non-homeobox region of hoxb13 predicted 21 nssnp’s to be potentially deleterious. among 123 utr snps analysed by utrscan, rs543028086, rs550968159, rs563065128 were found to affect the unr_bs, gy-box and mbe utr signals, respectively. subsequent analysis by polymirts revealed 23 utr snps altering the mirna […]


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UTRScan institution(s)
Istituto Tecnologie Biomediche del Consiglio Nazionale delle Ricerche (CNR), Bari, Italy; Dipartimento di Biochimica e Biologia Molecolare ‘E. Quagliariello’, Universita di Bari, Bari, Italy; Dipartimento di Chimica Strutturale e Stereochimica Inorganica, Universita degli Studi di Milano, Milano, Italy; Telethon Institute of Genetics and Medicine, Naples, Italy; Dipartimento di Scienze Biomolecolari e Biotecnologie, Universita di Milano, Milano, Italy
UTRScan funding source(s)
Supported by Ministero dell’Istruzione, dell’Universita e della Ricerca, Italy: Fondo Italiano Ricerca di Base, Italy: ‘Laboratorio Internazionale di Bioinformatica’ (LIBI); Laboratorio di Bioinformatica per la Biodiversita Molecolare (MBLAB).

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