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This option allows to search for desired target genes by gene identifier or sequence input (but not by both at the same time).


Select type of RNAi reagent

See image below:

  • 'long dsRNAs': for the design of long dsRNAs (including esiRNAs)
  • 'siRNAs': for the design of short interfering dsRNAs

Select organism

Here the organism used for the RNAi experiment is selected (see image below).



Search by gene identifier

The type of gene identifiers depends on the database, where the annotations were retrieved from:

  • For D. melanogaster (from FlyBase) FBgn and CG identifiers as well as gene symbols will work (e.g. CG11992, FBgn0014018 or rel)
  • For A. pisum (from AphidBase) ACYPI, XM and LOC identifiers will work (from 'official gene consensus set', e.g. ACYPI006699, XM_001944230 or LOC100165774)
  • For H. sapiens (from NCBI RefSeq) gene names, Entrez gene identifiers and RefSeq identifiers (e.g. RPS11, 6205 or NM_001015.3) will work
  • For S. mediterranea (from SmedGD) MAKER identifiers (mk4) will work (e.g. mk4.023206.00)
  • For S. cerevisiae and S. pombe (from EnsemblFungi) Ensembl gene identifiers will work (e.g. YHR055C for budding yeast, SPMIT.05 for fission yeast)
    For C. elegans (from WormBase) WBGene identifiers, sequence names and gene names will work (e.g. WBGene00006763, JC8.10 or unc-26)

In the image above the D. melanogaster gene wls was queried for the design of long dsRNAs. After submitting the query, E-RNAi shows the queried target genes as genome browser visualization including annotated isoforms and exons. Now sequences for the complete target gene, whole transcripts or certain exons can be selected as target sites. In the image below the exon wls:3 was selected as target site. The selection of multiple sequences is possible.



The 'Submit Selection' button leads to the settings page.


Paste or upload a sequence

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