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Protocols

psRNATarget specifications

Information


Unique identifier OMICS_00414
Name psRNATarget
Interface Web user interface
Restrictions to use None
Computer skills Basic
Stability Stable
Maintained Yes

Maintainer


  • person_outline Patrick Zhao

Additional information


http://plantgrn.noble.org/psRNATarget/help

Publications for psRNATarget

psRNATarget citations

 (110)
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Genome wide analysis of the SPL/miR156 module and its interaction with the AP2/miR172 unit in barley

2018
Sci Rep
PMCID: 5935748
PMID: 29728569
DOI: 10.1038/s41598-018-25349-0
call_split See protocol

[…] //weblogo.threeplusone.com/) was used to create the sequence logo of the barley SBP domain. The genomic and cDNA sequences of HvSPLs were analysed to predict the putative target sites of miR156 using psRNATarget tool (http://plantgrn.noble.org/psRNATarget/?function). Information on alternative splice events for each HvSPL gene was obtained from the Ensemble database (http://plants.ensembl.org/Hord […]

library_books

Molecular Characterization of SQUAMOSA PROMOTER BINDING PROTEIN LIKE (SPL) Gene Family in Betula luminifera

2018
Front Plant Sci
PMCID: 5945835
PMID: 29780401
DOI: 10.3389/fpls.2018.00608

[…] een confirmed that a subset of SPL genes are regulated by miR156 at posttranscriptional level in plant (Schwarz et al., ; Wang et al., , ; Jiao et al., ; Wang and Wang, ; Tripathi et al., ). With the psRNATarget online tool, a total of 12 BlSPLs were predicted to be targeted by miR156 (Figure ).The complementary sites of miR156 are in coding regions for nine BlSPLs (BlSPL1, BlSPL6, BlSPL7, BlSPL8, […]

call_split

Lateral Root Development in Potato Is Mediated by Stu mi164 Regulation of NAC Transcription Factor

2018
Front Plant Sci
PMCID: 5884874
PMID: 29651294
DOI: 10.3389/fpls.2018.00383
call_split See protocol

[…] The miRNA sequences of potato were obtained from the miRNA registry miRBase (). The target genes of Stu-mi164 were predicted using online program psRNATarget (). WMD3 (Web app for the automated design of artificial microRNAs) was use to design Stu-mi164 cloning primers. Sequence of potato and Arabidopsis NAC family TFs were obtained from plant […]

library_books

Genome wide identification, putative functionality and interactions between lncRNAs and miRNAs in Brassica species

2018
Sci Rep
PMCID: 5862966
PMID: 29563515
DOI: 10.1038/s41598-018-23334-1

[…] s visualized using Circos. To evaluate the lncRNAs that may act as precursors of miRNAs, we aligned the lncRNAs with identified miRNAs (e-value = 1e-5). lncRNAs as targets of miRNAs were predicted by psRNATarget (http://plantgrn.noble.org/psRNATarget/) with default values. The rate of non-synonymous substitutions (Ka) and the rate of synonymous substitutions (Ks) of coding genes were determined by […]

library_books

The mRNA and miRNA transcriptomic landscape of Panax ginseng under the high ambient temperature

2018
BMC Syst Biol
PMCID: 5861484
PMID: 29560829
DOI: 10.1186/s12918-018-0548-z

[…] To search for gene regulatory miRNAs, we identified target contigs of predicted miRNAs using psRNATarget []. psRNATarget is a small RNA target analysis tools for plant species. For the miRNA sequence input, we provided the known, conserved and novel miRNAs that are present in our small RNA-se […]

library_books

Identification of microRNAs involved in lipid biosynthesis and seed size in developing sea buckthorn seeds using high throughput sequencing

2018
Sci Rep
PMCID: 5838164
PMID: 29507325
DOI: 10.1038/s41598-018-22464-w

[…] buckthorn genome has not as yet been published, we determined the de novo mRNA transcriptome of seeds from four developmental stages of ‘SJ1’ and ‘XE3’ for identification of miRNA target genes. Using psRNATarget (plant miRNA target prediction server), 3074 gene targets were predicted. Some genes were targeted with multiple miRNA, leading to a total of 5594 putative miRNA-target interactions. The i […]

Citations

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psRNATarget institution(s)
Bioinformatics and Computational Biology Lab, Noble Research Institute, Ardmore, OK, USA
psRNATarget funding source(s)
Supported by the National Science Foundation [DBI-0960897 and DBI1458597]; Noble Research Institute.

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