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GenScript siRNA Target Finder

Algorithm parameters

Methods: Statistical Model (pattern:AAN19)
GC% Range from to
Max hits:

Maximal number of condidate siRNAs. It depends on the below option,Identical match.

Asmmetrey of double strands of the siRNA duplex >:
Identical match:

Candidate siRNA which matches more than entered number of bases against target gene will be left out.

Sequence Region Options:

Select from
Select from to

Off target filter

Study Organism:

Off target prediction of current release of our design tool is only suitable to human, mouse and rat.

Study Organ:

This option is valid if and only if the entrys human,mouse and rat in the above option are chosed. Entry "house" represents housekeeping genes which are expressed in all or near all tissues.

Size of seed region:

Previous investigations and GenScript experiment data show that siRNA "off target" transcript silencing mediated by seed region sequence is widespreed. "seed region" of siRNA is analogous to seed region of microRNA. GenScript resourchers found that size of seed region plays a major part in off target prediction. Size of seed region of siRNA we proposed is 6-8 bases.

Functional alignment:

Besides general sequence alignment, GenScript siRNA design tool incorporates a novel alignment approach, functional alignment. This idea for functional aligment derives from asymmetry of siRNA in the assembly of the RNAi enzyme complex.

Antiviral motif filter

Positive motif:

Positive motifs is a group of motifs which can significantly influence the in vivo application of siRNA owing to off target effects and toxicities associated with innate immunte stimulation. Therefore, siRNA containing positive motifs will be suppressed, in the other hand, siRNA containing negative motifs will be given a bonus.

Negative motif:

Antiviral motif filter

Tradeoff:

GenScript guarantees that 95% of off target effect will be filtered if all fitering conditions are chosed. However, some candidate siRNAs with highest knockdown efficiency are filtered owing to carry out a very strict screening conditions. Therefore, we should make a tradeoff between off-target effect and gene knockdown efficiency.

Enter your sequence

Paste in your target cDNA sequence (you can search in our ORF database to find your target cDNA sequence).