Predicted Off-targets for siRNA "ggucgaaacgccuaucagaaa" 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

5 hits were found for UCGAAACGCCUAUCAGAAA (2 guide strand hits and 3 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_001381 DOK1 367 385 cCGAAACGCCUuUCcGAAA39 3 10   false   <90%   1908
NM_002649 PIK3CG 1158 1176 gCGAAACGCCcAUCAaAAA10 3 9 c false   <90%   5379


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
XM_001129414 LOC731751 7824 7842 aUUCUGAUuGGCGUUUCcg30 4 8 c false   <90%   12650
NM_001081640 PRKDC 7832 7850 aUUCUGAUuGGCGUUUCcg30 4 8 c false   <90%   13416
NM_006904 PRKDC 7832 7850 aUUCUGAUuGGCGUUUCcg30 4 8 c false   <90%   13509


3 prime UTR Seed matches

Hits to same gene : 0
Hits to other genes : 251
View matched accessions

3 prime seed match details

AccessionGene nameHits to this gene
NM_199050C21orf252
NM_015500C21orf252
XM_001126965LOC7283822
NM_018351FGD61
NM_012215MGEA51
NM_001100ACTA11
NM_024416OGN1
NM_014057OGN1
NM_033014OGN1
NM_001001709FLJ455371
NM_005431XRCC21
NM_152716FLJ368741
NM_016206VGLL31
NM_002959SORT11
NM_014170GTPBP81
NM_138485GTPBP81
NM_178509STXBP41
NM_207380FLJ433391
NM_004921CLCA31
XM_001134426C12orf371
XM_001134418C12orf371
NM_018347C20orf291
NM_001040694INCENP1
NM_020238INCENP1
NM_198722AMIGO31
NM_145019FAM124A1
NM_001116ADCY91
XM_001132559LOC7322901
XM_001128665LOC7288691
NM_006234POLR2J1
NM_182506MAGEB101
NM_014388C1orf1071
NM_018079SRBD11
XM_001133595LOC7293241
XM_001133813LOC7317571
NM_014423AFF41
NM_014936ENPP41
NM_032554GPR811
NM_001037331LOC2842741
NM_006742PSKH11
NM_138393REEP61
NM_002766PRPSAP11
NM_0333901
NM_145206VTI1A1
NM_014007ZBTB431
NM_030665RAI11
NM_003851CREG11
NM_018425PI4KII1
NM_018469TEX21
XM_376795FLJ458721
XM_940037FLJ458721
NM_032020FUCA21
NM_198715PTGER31
NM_001039999FAM83G1
NM_021240DMRT31
NM_001010851ZNF7661
NM_181785SLC46A31
NM_018292QRSL11
NM_138348FAM105B1
NM_178505TMEM261
NM_145014HYLS11
NM_005742PDIA61
NM_013302EEF2K1
NM_020859SHROOM31
NM_004852ONECUT21
NM_002938RNF41
NM_194272RBPMS21
NM_020699GATAD2B1
NM_000130F51
NM_012429SEC14L21
NM_002725PRELP1
NM_201348PRELP1
NM_183397PXMP41
NM_007238PXMP41
NM_001718BMP61
NM_018008FEZF21
NM_199262SP61
NM_014899RHOBTB31
NM_147134NFX11
NM_024533CHST51
NM_152460C17orf771
NM_007295BRCA11
NM_007302BRCA11
NM_007304BRCA11
NM_007297BRCA11
NM_007296BRCA11
NM_007300BRCA11
NM_007305BRCA11
NM_007294BRCA11
NM_007299BRCA11
NM_007303BRCA11
NM_007298BRCA11
NM_024701ASB131
XM_001130036LOC7308151
XM_001132008LOC7287691
NM_178544ZNF5461
NM_052811TRIM131
NM_213590TRIM131
NM_001007278TRIM131
NM_005798TRIM131
NM_004319ASTN11
NM_005755EBI31
NM_005516HLA-E1
XM_379378LOC4012201
NM_004866SCAMP11
NM_001039570KREMEN11
NM_001039571KREMEN11
NM_198542ZNF7731
XM_001132013ANKH1
NM_054027ANKH1
NM_020375C12orf51
NM_001466FZD21
NM_003617RGS51
NM_207309UAP1L11
NM_152913TMEM1301
XM_001129510LOC7288621
XM_001129401LOC7311491
NM_001008404LOC4002581
NM_001078651TMEM1341
NM_025124TMEM1341
NM_001078650TMEM1341
NM_020804PACSIN11
NM_006079CITED21
NM_0010992721
NM_152733BTBD91
NM_0528931
NM_152914MGC338941
NM_012082ZFPM21
NM_194329RNF381
NM_194328RNF381
NM_194330RNF381
NM_022781RNF381
NM_194332RNF381
NM_005647TBL1X1
XM_932529LOC6449491
XM_943887LOC6449491
NM_207335KLHDC61
NM_004730ETF11
NM_002941ROBO11
NM_133631ROBO11
NM_033083EAF11
NM_016298FBXO401
NM_003221TFAP2B1
NM_199344SFT2D21
NM_001007102L3MBTL31
NM_032438L3MBTL31
NM_000594TNF1
NM_001024855ZNF1971
NM_032049AGTR11
NM_031850AGTR11
NM_004835AGTR11
NM_000685AGTR11
NM_009585AGTR11
XM_001134172LOC7300341
XM_001133186LOC7313451
NM_182894CHX101
NM_004237TRIP131
NM_024607PPP1R3B1
NM_018124RFWD31
NM_017526LEPROT1
NM_001949E2F31
NM_139321ATRN1
XM_001134344FLJ374531
NM_024577SH3TC21
NM_016305SS18L21
NM_014630ZNF5921
NM_001034852SMOC11
NM_022137SMOC11
NM_001453FOXC11
NM_178497C4orf261
NM_032842FLJ148031
NM_002499NEO11
NM_018100EFHC11
NM_020200PRTFDC11
NM_031439SOX71
NM_014877HELZ1
NM_032221CHD61
NM_003714STC21
NM_182848CLDN101
NM_006984CLDN101
NM_016622MRPL351
NM_001014380KATNAL11
NM_032116KATNAL11
NM_005358LMO71
XM_001129287LOC7308281
XM_001130324LOC7287371
NM_002416CXCL91
NM_183230IKZF31
NM_183229IKZF31
NM_183231IKZF31
NM_183228IKZF31
NM_183232IKZF31
NM_012481IKZF31
NM_001040280CD831
NM_004233CD831
NM_030648SETD71
NM_012309SHANK21
NM_0010400611
NM_144580C1orf851
XM_001133149LOC7314861
NM_052916RNF1571
NM_175907ZADH21
XM_001125952LOC7278521
XM_001132609LOC7313661
NM_003161RPS6KB11
NM_0011045581
NM_024930ELOVL71
XM_001127097LOC7282901
XM_001126346LOC7305611
NM_001554CYR611
NM_133330WHSC11
NM_001042424WHSC11
NM_133331WHSC11
NM_133335WHSC11
NM_025214CCDC681
NM_182700SP81
NM_198956SP81
NM_006699MAN1A21
NM_133448TMEM132D1
NM_003679KMO1
NM_004934CDH181
NM_0011024211
NM_0011024201
NM_006007ZFAND51
XM_001130020KIAA11471
XM_001130081KIAA11471
NM_001080392KIAA11471
NM_030647JHDM1D1
NM_203390RBM12B1
NM_003413ZIC31
NM_032042C5orf211
NM_002760PRKY1
NM_017437CPSF21
NM_025243SLC19A31
XM_001131408LOC7303501
XM_001127666LOC7308961
NM_148177FBXO321
NM_058229FBXO321
NM_153809TAF1L1
XM_375443LOC2841001
NM_020651PELI11
NM_014005PCDHA91
NM_006811SERINC31
NM_178836LOC2011641
NM_004594SLC9A51
NM_031889ENAM1
NM_019593KIAA14341
NM_144607CYB5D11
NM_001039395C9orf681
NM_001009554MFAP3L1
NM_021647MFAP3L1

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