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


Page contents

Table of Contents


Selection of reagent and organism



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Select type of RNAi reagent

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Choose long dsRNAs for the design of long dsRNAs (including esiRNAs) or siRNAs for the design of short interfering RNAs.

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Select organism

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Select the organism used for the RNAi experiment.


Search by gene identifier

The types of available gene identifiers depend on the database, where the annotations were retrieved from:


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Organism

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Source

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Available query identifiers


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D. melanogaster

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FlyBase

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FBgn, CG identifiers and gene symbols (e.g. CG11992, FBgn0014018 or rel)

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A. pisum

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AphidBase

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ACYPI, XM and LOC identifiers (from 'official gene consensus set', e.g. ACYPI006699, XM_001944230 or LOC100165774)

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H. sapiens

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NCBI RefSeq

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Gene names, Entrez gene identifiers and RefSeq identifiers (e.g. RPS11, 6205 or NM_001015.3)

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S. mediterranea

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SmedGD

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MAKER identifiers (mk4, from SmedGD) will work (e.g. mk4.023206.00)

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S. cerevisiae, S. pombe

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EnsemblFungi

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Ensembl gene identifiers (e.g. YHR055C for budding yeast, SPMIT.05 for fission yeast)

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C. elegans

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WormBase

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WBGene identifiers, sequence names and gene names (e.g. WBGene00006763, JC8.10 or unc-26)

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C. briggsae

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WormBase

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WBGene identifiers, transcript identifiers (e.g. WBGene00032891, CBG11841)

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A. gambiae

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VectorBase

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AGAP gene identifiers (e.g. AGAP000009)

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A. aegypti

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VectorBase

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AAEL gene identifiers (e.g. AAEL000068)

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M. musculus

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NCBI RefSeq

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Gene names, Entrez gene identifiers and RefSeq identifiers (e.g. Axin1, 12005 or NM_009733.2)

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A. mellifera

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BeeBase

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GB gene identifiers (e.g. GB15421)

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T. castaneum

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BeetleBase

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TC and GLEAN-prediction gene identifiers (e.g. TC004684 or GLEAN_04684)


Examples with identifiers specific to the selected organism are available as direct links on top of the identifier text-box.

In the example below the D. melanogaster genes FBgn0014018, wls, CG2956 and CG99999 were 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. The selection of multiple sequences is possible. Queried identifiers that were not found in the database (here CG99999) are listed in red at the top of the page.





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


Paste or upload a sequence

E-RNAi can also be queried with sequences. It is recommended to paste sequences in FASTA format. Raw sequences can also be pasted, however a query sequence must not contain any newline (each newline is interpreted as new query by E-RNAi). Example sequences specific to the selected organism can be pasted in the sequence text-box by clicking the 'FASTA' or 'RAW' links.
Alternatively, sequences can also be uploaded from file. Files must contain sequences in FASTA format (*.fa, *.fasta and *.txt file extensions are allowed).

In the example below sequences from the genes Ras85D and Nc were pasted in FASTA format.



After submitting the query, E-RNAi shows the queried sequences as genome browser visualization (if they could be mapped).



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