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NetPlantGene specifications


Unique identifier OMICS_09617
Name NetPlantGene
Interface Web user interface
Restrictions to use None
Computer skills Basic
Stability Stable
Maintained Yes


  • Plants and Fungi
    • Arabidopsis thaliana


  • person_outline Soren Bruk

Publication for NetPlantGene

NetPlantGene citations


CLE peptide encoding gene families in Medicago truncatula and Lotus japonicus, compared with those of soybean, common bean and Arabidopsis

Sci Rep
PMCID: 5570945
PMID: 28839170
DOI: 10.1038/s41598-017-09296-w

[…] which could be the likely start codon. The modified sequence was re-entered into SignalP and a signal peptide was detected in most instances. Possible intron boundary sites were identified using the NetPlantGene Server (, and the nucleotide splice sites and resulting prepropeptides were compared with orthologous sequences. Sequence logo graphs of the CLE d […]


Targeting a heterologous protein to multiple plant organelles via rationally designed 5′ mRNA tags

J Biol Eng
PMCID: 3847293
PMID: 24011257
DOI: 10.1186/1754-1611-7-20

[…] P (smGFP) using Gibson assembly []. This modified GFP contains three site-directed mutations that increase the protein’s solubility and fluorescence intensity []. Based on splice site prediction with NetPlantGene [], we predicted that the processed spliceforms of TriTag-1 and TriTag 2 encodes for GFP variants containing regions for chloroplast targeting, peroxisomal targeting or neither. Splicefor […]


The Arabidopsis thaliana MHX gene includes an intronic element that boosts translation when localized in a 5′ UTR intron

J Exp Bot
PMCID: 3808313
PMID: 24006416
DOI: 10.1093/jxb/ert235

[…] wn later on that elimination of this potential cryptic splice site resulted in full and accurate splicing of the CAT1 intron (). Prediction of potential cryptic splice sites was carried out using the NetPlantGene Server ( The synthesized DNA fragment was used to replace the 5′ UTR and LI between the BglII site of the promoter and the Mva1269I site of GUS. […]


The Role of Canonical and Noncanonical Pre mRNA Splicing in Plant Stress Responses

Biomed Res Int
PMCID: 3591102
PMID: 23509698
DOI: 10.1155/2013/264314

[…] ng-specific signs. Splice sites in the Arabidopsis DNA and DNA of other eukaryotes can be detected using the GeneSplicer Web Interface [] found at or the NetPlantGene Server [] found at To compile and visualize the evidence for alternative splicing in plants, a comprehensive web-interfaced database ASIP [] foun […]


Diversification, Biogeographic Pattern, and Demographic History of Taiwanese Scutellaria Species Inferred from Nuclear and Chloroplast DNA

PLoS One
PMCID: 3511331
PMID: 23226402
DOI: 10.1371/journal.pone.0050844
call_split See protocol

[…] ons of each sequence were queried in the Nucleotide collection database at the National Center for Biotechnology Information website using the Nucleotide Basic Local Alignment Search Tool program and NetPlantGene server at the Center for Biological Sequence Analysis website ( All sequences were deposited in the NCBI nucleotide sequence database under the followin […]


Fast splice site detection using information content and feature reduction

BMC Bioinformatics
PMCID: 2638148
PMID: 19091031
DOI: 10.1186/1471-2105-9-S12-S8

[…] identify true splice sites among numerous false ones. Weight matrix methods (WMM) and methods based on Markov models are popular methods of this category. WMM was successfully adopted in methods like NetPlantGene [] and NNSplice []. Salzberg et al. and Zhang et al. [,], used a linear first order Markov model (MM1) also known as the weight array method (WAM) and they have achieved a good splice sit […]


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NetPlantGene institution(s)
Center for Biological Sequence Analysis, The Technical University of Denmark, DK, Lyngby, Denmark; Laboratoire Associé de l'INRA, VIB, University of Gent, Gent, Belgium

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