Predicted Off-targets for siRNA "cguaacuaaacagcacaag" 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

8 hits were found for CGUAACUAAACAGCACAAG (7 guide strand hits and 1 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_006306 SMC1A 9042 9060 aGaAACUAAACAGCAaAAG52 3 12 c false   <90%   9725
NM_016621 PHF21A 1632 1650 CaUAcCUAAACAGCACAAu32 3 13 bc false   <90%   3692
NM_052813 CARD9 2071 2089 CGUAAaUAAACAGCACggG10 3 10 c false   <90%   2136
NM_025252 RAPH1 771 789 aGUAACUAAuCAGCACAga7 4 8 c false   <90%   2394
NM_203365 RAPH1 771 789 aGUAACUAAuCAGCACAga7 4 8 c false   <90%   2782
NM_213589 RAPH1 771 789 aGUAACUAAuCAGCACAga7 4 8 c false   <90%   9615
NM_031309 SCRT1 3423 3441 CaUAACUAAgCAGCACAAu0 3 8 bc false   <90%   3552


Hits to Sense 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
XR_019558 LOC647307 1289 1307 aUUGUGCUGUUUAcUUAua70 4 12 c false   <90%   1342


3 prime UTR Seed matches

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

3 prime seed match details

AccessionGene nameHits to this gene

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