Predicted Off-targets for siRNA "cgaugaugcgccaaagaga" 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

7 hits were found for CGAUGAUGCGCCAAAGAGA (3 guide strand hits and 4 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_005066 SFPQ 1848 1866 aaAUGAgGCGCCAAAGAGA20 3 12 bc false   <90%   3071
NM_025134 CHD9 7661 7679 aGAUGAUGCaCCAAAGAGA15 2 9 bc false   <90%   11479
NM_032905 RBM17 500 518 uagUGAaGCGCCAAAGAGA0 4 12 bc false   <90%   2709


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
NM_004852 ONECUT2 2947 2965 UgcaUUUGGCGCAUCAUCG32 3 15 bc false   <90%   16142
NM_001042698 ZSWIM7 206 224 UCUCUUUGGCuCAUCAgCc10 3 10 c false   <90%   1878
NM_001042697 ZSWIM7 206 224 UCUCUUUGGCuCAUCAgCc10 3 10 c false   <90%   2008
NM_178831 GATS 819 837 UCUCUUUGGCaCAUCAgCc10 3 10 c false   <90%   3493


3 prime UTR Seed matches

Hits to same gene : 0
Hits to other genes : 287
View matched accessions

3 prime seed match details

AccessionGene nameHits to this gene
NM_001364DLG22
NM_032689ZNF6072
NM_020203MEPE1
NM_001005411FCGR2C1
NM_001005410FCGR2C1
NM_016399TRIAP11
NM_001080395AATK1
NM_133646ZAK1
NM_015554GLCE1
NM_1449931
NM_015696GPX71
NM_000599IGFBP51
NM_006122MAN2A21
NM_170740ALDH5A11
NM_001080ALDH5A11
NM_178483C20orf791
NM_014829DDX461
NM_000134FABP21
NM_0011003901
NM_152558IQCE1
NM_017590ZC3H7B1
NM_001024649CANX1
NM_001746CANX1
NM_032289PSD21
NM_0010992671
XM_001130518LOC7284851
XM_001133894LOC7319641
NM_014386PKD2L21
NM_004012DMD1
NM_004016DMD1
NM_004009DMD1
NM_004017DMD1
NM_000109DMD1
NM_004011DMD1
NM_004015DMD1
NM_004023DMD1
NM_004022DMD1
NM_004020DMD1
NM_004021DMD1
NM_004007DMD1
NM_004006DMD1
NM_004013DMD1
NM_004014DMD1
NM_004018DMD1
NM_004010DMD1
NM_139068MAPK91
NM_139069MAPK91
NM_033331CDC14B1
NM_003671CDC14B1
NM_001077181CDC14B1
NM_013361ZNF2231
NM_001012267CENPP1
NM_000864HTR1D1
NM_145034TOR1AIP21
NM_144984C10orf721
NM_003155STC11
NM_138440VASN1
NM_000849GSTM31
NM_0010853751
NM_006750SNTB21
NM_003455ZNF2021
NM_005596NFIB1
NM_032208ANTXR11
NM_024798SNX221
NM_003657BCAS11
XM_941733LOC6471151
XM_930136LOC6471151
NM_152362TNFAIP8L11
NM_012232PTRF1
NM_015210KIAA08021
NM_0153061
NM_144667FLJ328941
NM_194247HNRPA31
NM_181654CPLX41
NM_015520MAGI11
NM_001033057MAGI11
NM_001334CTSO1
NM_005909MAP1B1
NM_001001420SMAD51
NM_001001419SMAD51
NM_005903SMAD51
NM_004137KCNMB11
NM_004737LARGE1
NM_133642LARGE1
NM_001256CDC271
NM_004914RAB361
NM_005570LMAN11
NM_152434CWF19L21
NM_153266TMEM1511
XM_001133285TMEM1511
XM_001132528NPTX11
NM_002522NPTX11
NM_052904KLHL321
NM_001017970TMEM30B1
NM_005955MTF11
NM_144599NIPA11
NM_001012958DISC11
NM_022719DGCR141
NM_031961KRTAP9-21
NM_0319631
NM_199126ZNF585A1
NM_152655ZNF585A1
NM_030964SPRY41
NM_014331SLC7A111
NM_152384BBS51
XM_001131828BBS51
XM_001131846BBS51
NM_033389SSH21
NM_005056JARID1A1
NM_001042603JARID1A1
NM_005716GIPC11
NM_202469GIPC11
NM_202470GIPC11
NM_202494GIPC11
NM_202468GIPC11
NM_202467GIPC11
NM_005151USP141
NM_001037334USP141
XM_943073LOC6478691
NM_145304C7orf331
NM_001025092MBP1
NM_002385MBP1
NM_001025081MBP1
NM_001025090MBP1
NM_001025101MBP1
NM_194317LYPD61
NM_020738KIDINS2201
NM_001040701FUT61
NM_000150FUT61
NM_015035ZHX31
XM_943032LOC6478051
NM_001083913C10orf261
NM_017787C10orf261
NM_001776ENTPD11
NM_0010981751
NM_024653PRKRIP11
NM_005264GFRA11
NM_145793GFRA11
NM_018952HOXB61
NM_001001479SLC35E41
NM_014807TMEM241
NM_0152951
NM_015113ZZEF11
NM_017970C14orf1021
NM_199043C14orf1021
NM_0152831
NM_032329ING51
XM_941026ING51
XM_001126273LOC7277731
NM_001001931MTUS11
NM_001001924MTUS11
NM_020749MTUS11
NM_001001925MTUS11
NM_021954GJA31
NM_182919TICAM11
NM_177999ASB61
NM_017873ASB61
NM_017542POGK1
NM_015545PTCD11
NM_1522931
NM_006773DDX181
XM_001129290STARD91
XM_001129482STARD91
NM_006323SEC24B1
NM_001042734SEC24B1
NM_000876IGF2R1
NM_003238TGFB21
NM_032839DIRC21
NM_032239LARP21
NM_015219EXOC71
NM_001013839EXOC71
NM_033064ATCAY1
NM_000544TAP21
NM_005324H3F3B1
NM_002714PPP1R101
NM_173551ANKS61
NM_005036PPARA1
NM_001001928PPARA1
NM_003930SKAP21
NM_001037SCN1B1
NM_005883APC21
NM_005634SOX31
NM_001079877RASA41
NM_006989RASA41
XM_933066LOC6436961
NM_0010096101
NM_033393KIAA17271
NM_001766CD1D1
NM_002789PSMA41
NM_0011026671
NM_0011026681
NM_006043HS3ST21
NM_020800IFT801
NM_020429SMURF11
NM_181349SMURF11
NM_173676PNPLA11
NM_003722TP73L1
NM_007350PHLDA11
NM_002853RAD11
NM_133377RAD11
NM_203453PPAPDC21
NM_016235GPRC5B1
NM_001001331ATP2B21
NM_001683ATP2B21
NM_005910MAPT1
NM_016841MAPT1
NM_016834MAPT1
NM_016835MAPT1
NM_199461NANOS11
NM_020914RNF2131
NM_003247THBS21
NM_001033582PRKCZ1
NM_002744PRKCZ1
NM_001033581PRKCZ1
NM_015847MBD11
NM_015844MBD11
NM_002384MBD11
NM_015846MBD11
NM_005188CBL1
NM_004905PRDX61
NM_015865SLC14A11
NM_0010854111
NM_153013C5orf331
NM_014344FJX11
XM_001132119LOC2574071
XM_001129456LOC2574071
XM_930505LOC6456761
XM_941520LOC6456761
NM_001009922RCHY11
NM_001008925RCHY11
NM_015436RCHY11
NM_001008883CCT31
NM_005998CCT31
NM_001008800CCT31
XM_001125875LOC7278181
NM_0011026581
NM_001009609SPANXN31
NM_001009615SPANXN21
NM_006624ZMYND111
NM_005776CNIH1
NM_005756GPR641
NM_001079859GPR641
NM_001079858GPR641
NM_001079860GPR641
NM_025219DNAJC51
NM_032727INA1
NM_004976KCNC11
NM_001024611LOC3399771
XM_001133431LOC7292301
NM_000648CCR21
NM_003020SCG51
NM_002634PHB1
NM_003764STX111
NM_022128RBKS1
NM_139279MCFD21
NM_052957ACRC1
NM_003799RNMT1
NM_024817THSD41
XM_931359LOC3387581
XM_944677LOC3387581
NM_001029859KCTD211
NM_000068CACNA1A1
NM_177996EPB41L11
NM_012156EPB41L11
NM_002214ITGB81
NM_030763NSBP11
NM_014279OLFM11
NM_173642FAM80A1
NM_014867KBTBD111
NM_133374ZNF6181
XM_925959LOC6424461
XM_936370LOC6422191
XM_061890TRIM641
NM_138415PHF21B1
XM_940609FLJ250761
XM_059689FLJ250761
NM_181804PKIG1
NM_181805PKIG1
NM_007066PKIG1
NM_006936SUMO31
NM_001025100MBP1
NM_002833PTPN91
XM_001128975PTPN91
NM_006361HOXB131
NM_0010937721
NM_000222KIT1
NM_175575WFIKKN21

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