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E-RNAi specifications


Unique identifier OMICS_04732
Name E-RNAi
Interface Web user interface
Restrictions to use None
Input data A gene identifier or a sequence.
Input format FASTA,RAW
Output format HTML,GFF,AFF
Computer skills Basic
Version 3.2
Stability Stable
Maintained Yes


  • Invertebrates
    • Caenorhabditis elegans
    • Drosophila melanogaster
  • Plants and Fungi
    • Saccharomyces cerevisiae
    • Schizosaccharomyces pombe
  • Primates
    • Homo sapiens
  • Rodents
    • Mus musculus


  • person_outline Michael Boutros <>
  • person_outline Thomas Horn <>
  • person_outline E-RNAi Team <>

Additional information


Publications for E-RNAi

E-RNAi citations


Thiamethoxam Resistance in Aphis gossypii Glover Relies on Multiple UDP Glucuronosyltransferases

PMCID: 5893893
PMID: 29670540
DOI: 10.3389/fphys.2018.00322

[…] previously described by peng et al. (). based on the ugt sequences (supplementary data ) and the possible interference sites predicted with online prediction software (http://www.dkfz.de/signaling/e-rnai3/), we designed specific primers using dnaman 6.0 software (http://www.lynnon.com/dnaman.html). the gene fragments were amplified from cdna and cloned into pgem-t (promega, usa). the purified […]


RNA Interference (RNAi) Screening in Drosophila

PMCID: 5844339
PMID: 29487145
DOI: 10.1534/genetics.117.300077

[…] these include up-torr for evaluation and visualization of existing rnai constructs (), rsvp for browsing and evaluating rnai stock phenotypes (), next-rnai for library design and evaluation (), and e-rnai, a web service for rnai construct design and evaluation (). these tools also implement algorithms that assess target specificity and efficacy of reagents., a number of well-established cell […]


Reduction in Musca domestica fecundity by dsRNA mediated gene knockdown

PMCID: 5771563
PMID: 29342168
DOI: 10.1371/journal.pone.0187353

[…] were produced as previously described for the mosquito aedes aegypti []. template selection and design of efficient dsrna primers utilized the ernai web service [, http://www.dkfz.de/signaling/e-rnai3/] with standard parameters except for selection of “other organism” (musca data not available for query in the ernai tool), amplicon size range 150–250 bp, and primer output to include […]


Individual co variation between viral RNA load and gene expression reveals novel host factors during early dengue virus infection of the Aedes aegypti midgut

PMCID: 5752042
PMID: 29261661
DOI: 10.1371/journal.pntd.0006152

[…] dnase-treated rna purified from a pool of ae. aegypti midguts was used to produce a pcr template for dsrna synthesis. briefly, gene-specific pcr primers for dsrna preparation were designed () using e-rnai web-service v.3.2 [] with 21-bp length for sirna specificity prediction and default parameters otherwise. a 500-bp fragment of the gfp gene was amplified with specific primers () and cloned […]


Proteomic profiling of neuronal mitochondria reveals modulators of synaptic architecture

PMCID: 5659037
PMID: 29078798
DOI: 10.1186/s13024-017-0221-9

[…] homology of rat gene of interest and drosophila orthologue was determined by input into diopt (drsc integrative ortholog prediction tool []). off-target effects of candidate lines were assessed using e-rnai software []. candidate lines exhibited no off-target effects based on genetic mapping data and all displayed 97.21-100% efficiency for targeting the intended gene (ndufb8 = 97.75%; mitofilin =  […]


The Roles of β Integrin of Chinese Shrimp (Fenneropenaeus chinensis) in WSSV Infection

PMCID: 5535956
PMID: 28686185
DOI: 10.3390/ijms18071465

[…] above. mortality was recorded daily to determine the neutralization effect of pfcβint-er., based on the protocols described by lin et al. [] and the online software (http://www.dkfz.de/signaling/e-rnai3//), the open reading frame (orf) of fcβint dsrna from 1650 to 2320 bp was designed using t7 ribomax (promega, madison, wi, usa). agarose gel electrophoresis was performed to examine […]

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E-RNAi institution(s)
German Cancer Research Center, Division Signaling and Functional Genomics, Heidelberg, Germany
E-RNAi funding source(s)
Supported by Studienstiftung (to T.H., PhD fellowship); Deutsche Forschungsgemeinschaft and the Helmholtz Association (partial); EC FP7 Program (Grant 201666).

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