RegRNA protocols

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RegRNA specifications

Information


Unique identifier OMICS_00415
Name RegRNA
Interface Web user interface
Restrictions to use None
Computer skills Basic
Stability Stable
Maintained Yes

Publications for RegRNA

RegRNA in pipelines

 (2)
2018
PMCID: 5906699
PMID: 29706982
DOI: 10.3389/fpls.2018.00481

[…] with mega7 using the neighbor-joining method and the bootstrap consensus tree was inferred from 1000 replicates. the function prediction of transcription factor using planttfdb online tool, the regrna 2.0 online tool () was used to identifying the functional motifs and sites of rcap2. the cis-acting element analyses were completed using online software plantcare () and softberry ()., […]

2016
PMCID: 4964384
PMID: 27347941
DOI: 10.3390/ijms17071008

[…] site master list). to investigate if snps may alter splicing sites, or related regulatory regions such as exonic and/or intronic splicing enhancer/silencer (ese/ess and ise/iss) we used the web tool regrna 2.0 [], as previously described in scarpato et al. []. briefly, fasta files of the nucleotide sequences surrounding the polymorphic site (10 bp upstream and 10 bp downstream the snp) […]


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RegRNA in publications

 (124)
PMCID: 5941480
PMID: 29739315
DOI: 10.1186/s12863-018-0615-x

[…] deeper focused studies give way to open up the potential significant roles for ssrs in pre-mirnas.fig. 1fig. 2fig. 3, the 149 ssr bearing pre-mirnas identified in a. thaliana when subjected to regrna analysis, detected different functional rna regulatory motifs. among this, a most interesting and concurrent functional motif was splicing regulatory element (sre). the sres were found […]

PMCID: 5943274
PMID: 29743605
DOI: 10.1038/s41419-018-0541-x

[…] microrna. for instance, p53 increases mir-34 to inhibit stemness in colorectal cancer. however, none of the predicted mir34-binding sites were found in the 3′utr of the cd51 transcripts (http://regrna.mbc.nctu.edu.tw/index1.php). others have suggested that p53 restricts stemness in cancer cells by directly targeting downstream molecules. hong et al. demonstrated that the p53-p21 pathway […]

PMCID: 5930724
PMID: 29720189
DOI: 10.1186/s12943-018-0829-6

[…] bgc-823 cells (additional file : figure s3b). to identify the potential mirna targets of lncrna mt1jp, in silico analysis was performed by using both findtar3 (http://bio.sz.tsinghua.edu.cn/) and regrna (http://regrna.mbc.nctu.edu.tw/index1.php) databases, and jointly predicted that seven mirnas (mir-24, mir-107, mir-195, mir-298, mir-185, mir-92a-3p and mir-223-5p) may act as biological […]

PMCID: 5909270
PMID: 29673400
DOI: 10.1186/s13287-018-0861-x

[…] molecular sponge to impede micrornas (mirnas) from binding to the mrna targets and mediate their functions. the potential lncrna–mirna mutual binding sites were predicted by the bioinformatics tool (regrna2.0, fig. ). we focused on the interaction between lncrna-h19 and mir-199a-5p, and a dual luciferase reporter assay was performed to further corroborate the specific interplay […]

PMCID: 5907460
PMID: 29669595
DOI: 10.1186/s13058-018-0959-1

[…] each involving five replicates., potential microrna binding sites of uca1 were predicted by algorithms obtained from the segal laboratory (http://132.77.150.113/pubs/mir07/mir07_prediction.html), by regrna (http://regrna.mbc.nctu.edu.tw/html/prediction.html) and by online microrna software (http://www.microrna.org). putative mir-122-5p and mir-185-5p target genes were predicted using a mirna […]


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RegRNA institution(s)
Institute of Bioinformatics and Systems Biology, National Chiao Tung University, Hsin-Chu, Taiwan

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