Predicted Off-targets for siRNA "ggucgauguaugucuuguugc" 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 UCGAUGUAUGUCUUGUUGC (1 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_003813 ADAM21 698 716 agGAUGUAUuUCUUGUUGu-1 4 8 bc false   <90%   2406


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_004626 WNT11 1019 1037 GCAACAAGACAUcCAaCGg58 3 12   false   <90%   1927
NM_177531 PKHD1L1 6514 6532 cCAACAAGACAcACAUCau56 4 10   false   <90%   14017
NM_004530 MMP2 2034 2052 aCAAgAAGACAUACAUCuu38 4 12 c false   <90%   3546
NM_004061 CDH12 3681 3699 cCAACAAGAgAUACAUCcu7 4 8 c false   <90%   4164


3 prime UTR Seed matches

Hits to same gene : 0
Hits to other genes : 315
View matched accessions

3 prime seed match details

AccessionGene nameHits to this gene
NM_001008844DSP2
NM_004415DSP2
NM_015033FNBP12
NM_213633PSG41
NM_002780PSG41
NM_015202KIAA05561
NM_152643KNDC11
NM_144975SLFN51
NM_001004313LOC3883351
NM_006096NDRG11
NM_014848SV2B1
NM_024423DSC31
NM_018036C14orf1031
NM_021072HCN11
NM_152268PARS21
NM_024607PPP1R3B1
NM_024841FLJ142131
NM_015576ERC21
NM_005121THRAP11
NM_001065TNFRSF1A1
XM_001134002C17orf411
NM_024857ATAD51
NM_0212411
NM_145244DDIT4L1
NM_030802FAM117A1
NM_145687MAP4K41
NM_145686MAP4K41
NM_004834MAP4K41
NM_003749IRS21
NM_030641APOL61
NM_021079NMT11
NM_153033KCTD71
NM_021912GABRB31
NM_000814GABRB31
XM_379636C9orf1221
XM_940165C9orf1221
NM_198859PRICKLE21
XM_001132083LOC7321751
XM_001131915LOC7299671
NM_152900MAGI31
NM_003287TPD52L11
NM_001003395TPD52L11
NM_001003396TPD52L11
NM_001003397TPD52L11
NM_002522NPTX11
NM_005626SFRS41
NM_130834OPA11
NM_015560OPA11
NM_130836OPA11
NM_130831OPA11
NM_130832OPA11
NM_130837OPA11
NM_130833OPA11
NM_130835OPA11
NM_002610PDK11
NM_015104KIAA04041
NM_170662CBLB1
XM_001133002LOC7288041
NM_000367TPMT1
NM_001831CLU1
NM_203339CLU1
NM_002898RBMS21
NM_020746VISA1
NM_198274SMYD11
NM_017952PTCD31
NM_017671C20orf421
NM_031303KATNAL21
XM_001129888KATNAL21
NM_020131UBQLN41
NM_032740SFT2D31
NM_014953DIS31
NM_031445AMMECR1L1
NM_025152NUBPL1
NM_014701KIAA02561
NM_023037FRY1
XM_926521LOC6531371
XM_928267LOC6532701
XM_926348LOC6426331
NM_014647KIAA04301
NM_138554TLR41
NM_001077528FBXO431
NM_001029860FBXO431
NM_003968UBE1C1
NM_198195UBE1C1
NM_002337LRPAP11
NM_0011055731
NM_024594PANK31
XM_934166LOC6534411
NM_004426PHC11
NM_004960FUS1
NM_005614RHEB1
NM_130463ATP6V1G21
NM_138282ATP6V1G21
NM_014349APOL31
NM_145642APOL31
NM_145640APOL31
NM_145639APOL31
NM_030644APOL31
NM_145641APOL31
NM_001005920LOC3391231
XM_930823LOC6423351
NM_004055CAPN51
NM_182580CYB561D11
NM_016227C1orf91
NM_014283C1orf91
NM_032317WBSCR181
NM_153619SEMA6D1
NM_002193INHBB1
NM_004796NRXN31
NM_0011052501
NM_138970NRXN31
NM_012193FZD41
XM_943378LOC6423351
NM_006315PCGF31
NM_032642WNT5B1
NM_030775WNT5B1
NM_201628FLJ438061
NM_001039397FLJ402441
NM_001010846SHE1
NM_177454KIAA19461
NM_153633HOXC41
NM_014620HOXC41
NM_017548CDV31
NM_000031ALAD1
NM_001003945ALAD1
NM_214679CLEC4M1
NM_214678CLEC4M1
NM_214677CLEC4M1
NM_138733PGK21
NM_207395ZNF324B1
NM_014347ZNF3241
NM_005941MMP161
NM_130469JDP21
NM_032932RAB11FIP41
NM_016021UBE2J11
NM_000633BCL21
NM_178812MTDH1
NM_033655CNTNAP31
XM_001128489LOC7285771
NM_006578GNB51
NM_016194GNB51
NM_018085IPO91
NM_018361AGPAT51
NM_004603STX1A1
NM_000368TSC11
NM_018181ZNF5321
NM_182752FAM79A1
NM_004745DLGAP21
NM_207348SLC25A341
NM_006990WASF21
NM_003010MAP2K41
NM_078485COL9A11
NM_001851COL9A11
XM_001127417LOC6479091
XM_932285LOC6446521
XM_930805LOC6424261
NM_133459CCBE11
NM_002531NTSR11
NM_022719DGCR141
NM_181722LOC2859081
NM_198700CUGBP11
NM_006560CUGBP11
NM_001025596CUGBP11
NM_024334TMEM431
NM_0010096101
NM_000599IGFBP51
NM_024963FBXL181
NM_001196BID1
NM_197967BID1
NM_197966BID1
NM_023076C16orf281
NM_001080414KIAA15091
XM_496003KIAA15091
XM_941642KIAA15091
NM_032466ASPH1
NM_032468ASPH1
NM_001905CTPS1
NM_207333ZNF3201
NM_002792PSMA71
NM_014231VAMP11
NM_016830VAMP11
NM_199245VAMP11
NM_001879MASP11
NM_003216TEF1
NM_020825CRAMP1L1
NM_014850SRGAP31
NM_001033117SRGAP31
NM_145250RNASE111
NM_001081573GAB31
NM_080612GAB31
NM_006822RAB40B1
NM_0333901
NM_004842AKAP71
NM_138633AKAP71
NM_016377AKAP71
NM_194314ZBTB411
XM_944029LOC6479791
NM_0011055411
NM_005382NEFM1
NM_032199ARID5B1
NM_001080484KIAA17511
NM_001609ACADSB1
NM_018357LARP61
NM_006955ZNF33B1
NM_006974ZNF33A1
NM_006954ZNF33A1
NM_001621AHR1
NM_175698SSX21
NM_003147SSX21
NM_005036PPARA1
NM_001001928PPARA1
NM_005635SSX11
NM_173358SSX71
XM_001125936LOC7278371
NM_174962SSX91
NM_021015SSX51
NM_175723SSX51
NM_153048FYN1
NM_002037FYN1
NM_153047FYN1
NM_020772NUFIP21
NM_025224ZBTB461
NM_002665PLGLB21
NM_001032392PLGLB11
NM_173469UBE2Q21
NM_002998SDC21
NM_016929CLIC51
NM_001032396PJA11
NM_145119PJA11
NM_022368PJA11
NM_181458PAX31
NM_181460PAX31
NM_181457PAX31
NM_181459PAX31
NM_014813LRIG21
NM_000210ITGA61
NM_001079818ITGA61
NM_018207TRIM621
NM_139283PPTC71
NM_002747MAPK41
NM_153365TAPT11
NM_006266RALGDS1
NM_001042368RALGDS1
NM_000926PGR1
NM_007146VEZF11
NM_203380ACSL51
NM_203379ACSL51
NM_016234ACSL51
NM_152278TCEAL71
NM_175883OR7D21
NM_018639WSB21
NM_175729SSX41
NM_005636SSX41
NM_001040612SSX4B1
NM_001034832SSX4B1
NM_173357SSX61
NM_153188TNPO11
NM_002270TNPO11
NM_019885CYP26B11
NM_001280CIRBP1
NM_000791DHFR1
XM_001133837LOC7320991
XM_001133987LOC7296811
NM_1735691
NM_020940KIAA16001
NM_017658KLHL281
NM_020742NLGN4X1
NM_181332NLGN4X1
NM_020445ACTR3B1
NM_001040135ACTR3B1
NM_020738KIDINS2201
NM_025010KLHL181
NM_006335TIMM17A1
NM_000963PTGS21
NM_006290TNFAIP31
NM_019012PLEKHA51
NM_001014283DCUN1D21
NM_001037494DYNLL11
NM_001037495DYNLL11
NM_003746DYNLL11
NM_001076786QSER11
NM_003131SRF1
NM_001083591CUGBP21
NM_001025077CUGBP21
NM_006561CUGBP21
NM_001025076CUGBP21
NM_198904GABRG21
NM_000816GABRG21
NM_198903GABRG21
NM_177452TRAPPC6B1
NM_001079537TRAPPC6B1
NM_004286GTPBP11
NM_012275IL1F51
NM_173170IL1F51
NM_002207ITGA91
NM_014646LPIN21
NM_016399TRIAP11
NM_021648TSPYL41
NM_203406LOC1533641
NM_014141CNTNAP21
NM_001031711ERGIC11
NM_002111HD1
NM_005499SAE21
NM_005895GOLGA31
NM_001042492NF11
NM_000267NF11
NM_004992MECP21
NM_015064ERC11
NM_178039ERC11
NM_178040ERC11
NM_178038ERC11
NM_178037ERC11
NM_032832LRP111
NM_005238ETS11
XM_001126762LOC7281761

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