Predicted Off-targets for siRNA "gucggucgagaauacgcugug" Using siRNA SpecificityServer

Specificity Server [Result page v1.0]


SpecificityServer - An siRNA design program for determining siRNA specificity

Automatic recommendation
OK - siRNA is specific for both sense and antisense (guide) strands

1 hit was found for CGGUCGAGAAUACGCUGUG (1 guide strand hits and 0 sense strand hits.)

Hits to Guide strand

AccessionGeneStartEndDetails of mismatchesSpec.
Score
MismatchesContiguousJackson style
specificity
Hits similar
gene
HSP
Score
HSP %
Identity
HSP lengthGene Length
1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19
NM_006219 PIK3CB 1854 1872 CGuUCGAGAAUAuGCUGUa65 3 9   false   <90%   3213



3 prime UTR Seed matches

Hits to same gene : 0
Hits to other genes : 32
View matched accessions

3 prime seed match details

AccessionGene nameHits to this gene
NM_033225CSMD11
XM_925839LOC1583011
NM_001024858SPTB1
NM_003480MFAP51
NM_175932PSMD131
NM_002817PSMD131
XM_929433LOC6440061
XM_939111LOC6500201
NM_002938RNF41
NM_015949C7orf201
NM_144999LRRC451
NM_017637BNC21
NM_145647WDR671
NM_173814PRTG1
NM_000623BDKRB21
NM_007260LYPLA21
XM_001125935LOC7304801
XM_001125965LOC7278871
NM_153025C16orf551
XM_941026ING51
XM_001126273LOC7277731
NM_032329ING51
NM_001001852PIM31
XM_938171PIM31
NM_022568ALDH8A11
NM_170771ALDH8A11
NM_015191SNF1LK21
NM_018683ZNF3131
NM_013255MKLN11
XM_377073LOC3764751
NM_022719DGCR141
NM_024963FBXL181

Immunostimulatory motif search results


UGUGU - Judge et al. Sequence-dependent stimulation of the mammalian innate immune response by synthetic siRNA. Nat Biotechnol. 2005 Apr;23(4):457-62. (PMID: 15778705)
No Immunostimulatory motif found (UGUGU).

GUCCUUCAA - Hornung et al. Sequence-specific potent induction of IFN-alpha by short interfering RNA in plasmacytoid dendritic cells through TLR7. Nat Med. 2005 Mar;11(3):263-70. Epub 2005 Feb 20. (PMID: 15723075)
No Immunostimulatory motif found (GUCCUUCAA).



Settings used for search

Scores were calculated using scoring scheme SS1
Using AVG scoring mode.

Hit scores

ParameterSpec. Score cut-offColourComment
Hit to same geneColourHits to the same accession or genes with 100 percent identity (i.e. likely transcript variants). It is advisable to always check the genes hit.
High scoring hit≥80ColourHits are very likely to cause an off-target effect
Medium scoring hit<80¸≥40ColourHits with a small chance of causing an off target effect.
Low scoring hitColourHits very unlikely to cause an off-target effect

The mismatches are colour coded based on the weighting of that position.

Cut-offColour
MatchColour
Wobble base pairs (G-U)Colour
Critical bases (none)Colour
0.6 bitsColour
0.4 bitsColour
0.2 bitsColour

About SpecificityServer

SpecificityServer is designed to help you identify potential non-specific matches to your siRNA. It incorporates the latest information about non-specific matches (sequence-specific only).

Designed by: Alistair Chalk, Quan Du, Zicai Liang and Erik L.L. Sonnhammer


For more details about the algorithm "siRNA specificity searching incorporating mismatch tolerance data" Bioinformatics (2008) 24 (10): 1316-1317