siSPOTR is a RNAi design tool that produces candidate siRNAs and shRNA with the lowest off-targeting potential for a given target transcript. Instructions
- Input sequence(s) for siRNA design. Click
the appropriate button to paste or upload the sequence(s). Single
sequences can be in plain or FASTA format. Multiple sequences
require FASTA formatting.
- Select the number of candidates desired in
- (Advanced) Modify input parameters:
- GC Content (%Min/Max): Filters candidate
sequences based on specified GC content range.
- 5' Passenger G/C Number: Forces the
passenger strand to have high 5' end stability. This decreases
likelihood of loading the unintended (passenger) strand.
Additional parameters to promote guide strand loading are
automatically included in the design.
- Pol III Expression: Removes sequences
with ≥4 T/U's. Stretches of 4 or more U's can serve as a
termination signal for RNA Pol III. Since many shRNA/artificial
miRNA expression vectors use Pol III promoters (e.g. U6, H1) to
drive expression, these sequences should be avoided to prevent
pre-mature transcript termination.
- Run siSPOTR
- Browse additional off-target information
(Highly Recommended): Click "Off-Target Details" to:
- BLAST against transcript databases
- View the overall number of off-targets and the
distribution of more potent seed site-types (7mer-1A, 7mer-M8,
- View/download list of all predicted off-targets with