RNAi Target Sequence Selector

Enter a cDNA sequence or an accession number (RefSeq and GenBank are accepted) for your gene of interest to generate a list of candidate sequences that can be targeted by RNAi.

Note, the site utilizes the XEMBL web service of the EBI to obtain sequences for GenBank accession numbers. If the XEMBL service is not available then you will not be able to design against a GenBank accession - try again later.

Accession Number   (example: NM_000546)
(min length
75 nr)
Number to return
Sort by
Hairpin max Tm
Optimal GC(%)
Selection criteria
Tm(5') > Tm(3') by
Max polyN   Low complexity filter
Selection rules AA at [-1,0] A at 3 A at 6
T at 10 No G at 13 AA at [18,19]
at least one A or T at [18,19]


Potential RNAi target sequences

The following 19-base sequences are potential siRNAs specific to the entered sequence of the length bp.
Click on the sequence to design an shRNA species.

  Sequence Position GC(%) HpTm(C) dTm(C) Blast Search


Note that the tool does not perform any sequence similarity searches to ensure the specificity of the RNAi target. A link is given to the NCBI BLAST server enabling a similarity search of the suggested target against the mRNA database of the organism of interest.