Predicted Off-targets for siRNA "gauccugcgcgggacguccuu" 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 UCCUGCGCGGGACGUCCUU (4 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_170726 ALDH4A1 1668 1686 UCCUGCGCuGGACGUCgcc8 4 8 c false   <90%   2147
NM_003748 ALDH4A1 1668 1686 UCCUGCGCuGGACGUCgcc8 4 8 c false   <90%   3160
NM_002161 IARS 2079 2097 gggUGuGCGGGACGUCCUU3 4 13 bc false   <90%   4403
NM_013417 IARS 2186 2204 gggUGuGCGGGACGUCCUU3 4 13 bc false   <90%   4510


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_939821 DKFZp781N1041 494 512 AAcGACGUuCCGCGCAGGc15 3 9 bc false   <90%   1407
XM_370577 DKFZp781N1041 494 512 AAcGACGUuCCGCGCAGGc15 3 9 bc false   <90%   1407
NM_145214 TRIM11 997 1015 AAGGACGcCCuGCGCAGGg-28 3 7 c false   <90%   2715


3 prime UTR Seed matches

Hits to same gene : 0
Hits to other genes : 673
View matched accessions

3 prime seed match details

AccessionGene nameHits to this gene
NM_177999ASB63
NM_001001852PIM33
XM_938171PIM33
NM_002501NFIX3
NM_015894STMN32
NM_001003674C18orf12
NM_181483C18orf12
NM_181481C18orf12
NM_001003675C18orf12
NM_004338C18orf12
NM_181482C18orf12
XM_933796SLC45A42
XM_936706KLHL172
NM_198317KLHL172
NM_002430MN12
NM_015094HIC22
NM_018389SLC35C12
XM_941665LOC3877632
XM_373497LOC3877632
NM_031475ESPN2
NM_0011127042
NM_020714ZNF4902
NM_014694ADAMTSL22
NM_004286GTPBP12
NM_007101SARDH1
NM_133448TMEM132D1
NM_001535PRMT21
NM_206962PRMT21
NM_001030288SPN1
NM_003123SPN1
NM_004561OVOL11
XM_001129344OVOL11
NM_025191EDEM31
NM_182580CYB561D11
NM_0333901
NM_153246MGC454911
NM_002980SCTR1
NM_153608ZNF1141
NM_153029N4BP11
NM_004496FOXA11
NM_001040647RCP91
NM_001040648RCP91
NM_014478RCP91
XM_940107TSPAN111
NM_001080509TSPAN111
NM_024893C20orf391
NM_006047RBM121
NM_152838RBM121
NM_001077UGT2B171
XM_001125683UGT2B171
NM_003603SORBS21
NM_021069SORBS21
NM_006031PCNT1
NM_032052PATZ11
NM_004227PSCD31
NM_033302ADRA1A1
NM_152393KBTBD51
NM_022497MRPS251
NM_024577SH3TC21
NM_021020LZTS11
NM_014016SACM1L1
NM_052968APOA51
NM_019601SUSD21
XM_001127668LOC7281191
XM_001131429LOC7311181
NM_004331BNIP3L1
NM_020859SHROOM31
NM_006555YKT61
NM_031910C1QTNF61
NM_182486C1QTNF61
NM_199162ADPRHL11
NM_138430ADPRHL11
NM_012306FAIM21
NM_014850SRGAP31
NM_001033117SRGAP31
NM_021064HIST1H2AG1
NM_001065TNFRSF1A1
NM_018245OGDHL1
NM_139071SMARCD11
NM_003076SMARCD11
NM_053055THEM41
XM_001133026LOC7313861
XM_001133204LOC7291201
NM_001024843TNRC6B1
NM_015088TNRC6B1
NM_030964SPRY41
NM_198147LOC1162361
NM_000040APOC31
NM_153051MTMR31
NM_021090MTMR31
NM_153050MTMR31
NM_178569C5orf381
NM_002547OPHN11
NM_005069SIM21
NM_006725CD61
NM_002730PRKACA1
NM_207518PRKACA1
NM_052846EMILIN31
NM_005061RPL3L1
NM_017540GALNT101
NM_198321GALNT101
NM_1522931
NM_005250FOXL11
NM_020223FAM20C1
NM_018189DPPA41
NM_001003407ABLIM11
NM_001003408ABLIM11
NM_002313ABLIM11
NM_006720ABLIM11
NM_004729ZBED11
NM_0011126631
NM_006629ZNF2711
NM_007175ERLIN21
NM_005098MSC1
NM_0011006261
NM_006459ERLIN11
NM_000695ALDH3B21
NM_001031615ALDH3B21
XM_001129292MBOAT21
NM_138799MBOAT21
NM_024701ASB131
NM_031477YPEL31
XM_379228LOC4010931
XM_944985LOC4010931
NM_006643SDCCAG31
NM_001039708SDCCAG31
NM_001039707SDCCAG31
NM_001013693LDLRAD21
NM_001080437SNED11
XM_940984SNED11
NM_153810C10orf461
NM_173477USH1G1
NM_001003698RREB11
NM_001003699RREB11
NM_002955RREB11
NM_177417KLC31
NM_004050BCL2L21
NM_182500C2orf501
NM_177963SYT121
NM_001310CREBL21
NM_145799SEPT61
NM_0190041
NM_0011049251
NM_018257PCMTD21
NM_182572ZSCAN11
NM_004930CAPZB1
NM_005028PIP5K2A1
NM_018425PI4KII1
NM_025083EDC31
NM_003687PDLIM41
NM_021116ADCY11
NM_005076CNTN21
XM_927712LOC4401041
NM_007006NUDT211
NM_006698BLCAP1
NM_022562GH11
NM_022557GH21
NM_144570HN1L1
NM_022644CSH21
NM_022640CSH11
NM_001503GPLD11
NM_144707PROM21
NM_182501MTERFD21
NM_182551LYCAT1
NM_001002257LYCAT1
NM_017451BAIAP21
NM_014883FAM13A11
NM_001015045FAM13A11
NM_020245TULP41
NM_001007466TULP41
XM_001126326AGRIN1
NM_198576AGRN1
NM_014507MCAT1
NM_173467MCAT1
NM_005629SLC6A81
NM_002073GNAZ1
NM_020372SLC22A171
NM_016609SLC22A171
NM_001754RUNX11
NM_001001890RUNX11
NM_0149871
NM_006553SLMO11
NM_003751EIF3S91
NM_001037283EIF3S91
NM_019885CYP26B11
NM_032266C2orf161
NM_021189CADM31
NM_0010994561
NM_000836GRIN2D1
NM_020134DPYSL51
NM_015720PODXL21
NM_006943SOX121
NM_001720BMP8B1
NM_206538LOC2843611
NM_175063LOC2843611
NM_016147PPME11
NM_178554KY1
NM_003840TNFRSF10D1
NM_032370ZNF4141
NM_020443NAV11
NM_001144AMFR1
NM_012231PRDM21
NM_005186CAPN11
NM_006424SLC34A21
NM_031287SF3B51
NM_005245FAT1
NM_022170EIF4H1
NM_031992EIF4H1
NM_004398DDX101
NM_006651CPLX11
NM_014424HSPB71
NM_005185CALML31
NM_000744CHRNA41
NM_030660ATXN31
NM_004993ATXN31
NM_001693ATP6V1B21
XM_943034LOC6430851
XM_931304LOC6430851
XM_001133756LOC7316011
XM_001133752LOC7294301
NM_002189IL15RA1
NM_172200IL15RA1
NM_033064ATCAY1
NM_002360MAFK1
NM_006176NRGN1
NM_001771CD221
XM_942692MGC51391
NM_001080533MGC51391
NM_025251KIAA16881
NM_152470RNF1651
NM_018316KLHL261
NM_000476AK11
NM_013269CLEC2D1
NM_001004419CLEC2D1
NM_032261C21orf561
XM_001126144LOC7305101
XM_942958LOC6422361
XM_943005LOC6422361
NM_183059RD31
NM_152547BTNL91
NM_024074TMEM38A1
NM_014763MRPL191
NM_020888KIAA15221
NM_004845PCYT1B1
NM_001078171FAM127A1
NM_001078173FAM127C1
NM_024915GRHL21
NM_001042498SLC35A21
NM_001032289SLC35A21
NM_001080849LOC7284891
NM_001083314CHMP1A1
NM_002768CHMP1A1
NM_000093COL5A11
NM_006688C1QL11
NM_024676C1orf1131
NM_005975PTK61
NM_020901KIAA15421
NM_021079NMT11
NM_145701CDCA41
NM_017955CDCA41
XM_001126784LOC7306801
XM_001128897LOC7286381
XM_001128905LOC7286381
XM_001126798LOC7306801
NM_002273KRT81
NM_001006641SLC25A251
NM_001006642SLC25A251
NM_052901SLC25A251
NM_001006643SLC25A251
NM_004831CRSP71
NM_015111N4BP31
NM_001008701LPHN11
NM_014921LPHN11
NM_033067DMRTB11
NM_152793C7orf411
XM_936719LOC6476621
NM_001748CAPN21
NM_033512TSPYL51
NM_004078CSRP11
NM_001010846SHE1
NM_033496HK11
NM_000188HK11
NM_033498HK11
NM_033500HK11
NM_033497HK11
NM_004583RAB5C1
NM_201434RAB5C1
NM_152694ZCCHC51
NM_004917KLK41
NM_018379FAM63A1
NM_022134GAL3ST21
NM_032575GLIS21
NM_017873ASB61
NM_199367SPG71
NM_181353ID11
XM_001128242LOC7287041
NM_005134PPP4R11
NM_001042388PPP4R11
NM_001259CDK61
NM_004045ATOX11
NM_004387NKX2-51
NM_001347DGKQ1
NM_004288PSCDBP1
NM_139246C9orf971
NM_014909VASH11
NM_020773TBC1D141
NM_020909EPB41L51
NM_002569FURIN1
NM_018027FRMD4A1
NM_000368TSC11
NM_012458TIMM131
NM_139015SPPL31
NM_016376ANKFY11
XM_499356LOC4426091
XM_935540LOC4426091
XM_499348MGC573591
XM_001127525LOC7303071
XM_496899LOC4412581
XM_929470LOC6439091
XM_001127430LOC7303041
NM_004391CYP8B11
NM_015102NPHP41
NM_182970RIMS41
NM_058238WNT7B1
NM_006116MAP3K7IP11
NM_002928RGS161
NM_017758ALKBH51
NM_0010992941
XM_936510KIAA16441
NM_014172PHPT11
NM_002883RANGAP11
NM_004716PCSK71
NM_181709FAM101A1
NM_000960PTGIR1
NM_152734C6orf891
NM_000588IL31
NM_033326SOX61
NM_017508SOX61
NM_148920PIGQ1
NM_004204PIGQ1
NM_014732KIAA05131
NM_182898CREB51
NM_004904CREB51
NM_001011666CREB51
NM_182899CREB51
NM_173516PNLDC11
NM_153266TMEM1511
XM_001133285TMEM1511
NM_0011099741
NM_018337ZNF4441
NM_032345WIBG1
NM_002725PRELP1
NM_201348PRELP1
NM_000727CACNG11
XM_938374LOC6440101
NM_002461MVD1
XM_001126137LOC2849521
XM_001129340LOC2849521
NM_203413C17orf811
NM_020531C20orf31
NM_018942HMX11
NM_0010992201
NM_001030010ALDH3B11
NM_000694ALDH3B11
NM_032538TTBK11
NM_000259MYO5A1
XM_001131803LOC7320781
NM_003924PHOX2B1
NM_2073061
NM_002390ADAM111
NM_015260SIN3B1
NM_0321101
NM_002014FKBP41
NM_014468VENTX1
NM_002896RBM41
XM_001126273LOC7277731
XM_941026ING51
NM_032329ING51
NM_017723C9orf1671
NM_001003806TARP1
NM_001003799TARP1
NM_212533ABCA21
NM_001606ABCA21
NM_139239TA-NFKBH1
NM_031409CCR61
NM_004367CCR61
NM_003636KCNAB21
NM_172130KCNAB21
NM_032017STK401
NM_133467CITED41
NM_017594DIRAS21
NM_1524191
NM_201397GPX11
XM_001131851LOC6490951
XM_001132597LOC6442351
NM_003824FADD1
NM_001277CHKA1
NM_212469CHKA1
NM_004759MAPKAPK21
NM_0150161
NM_001080415SR1401
XM_940802SR1401
NM_207397CD164L21
NM_015516TSKU1
NM_004193GBF11
NM_004040RHOB1
NM_000681ADRA2A1
NM_005229ELK11
NM_052880PIK3IP11
NM_005632SOLH1
NM_001409MEGF61
NM_032042C5orf211
NM_000376VDR1
NM_001017535VDR1
NM_020813ZNF4711
NM_022104C20orf671
XM_001132246LOC7299971
NM_032608MYO18B1
NM_0010976201
NM_183040DTNBP11
NM_003311PHLDA21
NM_033131WNT3A1
NM_001003406CACNA1I1
NM_021096CACNA1I1
NM_032484GHDC1
NM_002221ITPKB1
NM_139280ORMDL31
NM_018645HES61
NM_001014831PAK41
NM_001014835PAK41
NM_001014834PAK41
NM_005884PAK41
NM_001014832PAK41
NM_001077663URG41
NM_017920URG41
NM_001077664URG41
NM_020695REXO11
NM_080821C20orf1081
NM_001457FLNB1
NM_024105ALG121
NM_018670MESP11
NM_052861MGC216751
NM_000991RPL281
NM_181844BCL6B1
NM_002997SDC11
NM_001006946SDC11
NM_199454PRDM161
NM_022114PRDM161
XM_001134396LOC7302541
NM_001014431AKT11
NM_001014432AKT11
NM_005163AKT11
XM_001125753MUC3B1
NM_024811FLJ125291
NM_207514FLJ201861
NM_015690STK361
NM_001024401SBK11
NM_004474FOXD21
NM_145663DBF4B1
NM_001006638RAB371
NM_080865GPR621
NM_001030060SAMD51
NM_020319ANKMY21
NM_001006620MAPKAP11
NM_001006619MAPKAP11
NM_001006621MAPKAP11
NM_024117MAPKAP11
NM_001006617MAPKAP11
NM_014578RHOD1
NM_007349PAXIP11
NM_153837GPR1141
NM_175900C16orf541
XM_001128758LOC7280701
NM_018031WDR61
XM_001131164LOC7309711
NM_000950PRRG11
NM_003507FZD71
NM_020761KIAA13031
XM_001131117LOC7318821
XM_001130751LOC7296011
NM_016426GTSE11
NM_145115ZNF4981
NM_178557NAT8L1
NM_013242C16orf801
NM_032792ZBTB451
NM_006621AHCYL11
NM_001008408RBM331
NM_053043PRR81
NM_024896KIAA18151
NM_021155CD2091
NM_014600EHD31
NM_004290RNF141
NM_183400RNF141
NM_183398RNF141
NM_183401RNF141
NM_183399RNF141
NM_015509NECAP11
NM_203329CD591
NM_203331CD591
NM_203330CD591
NM_000611CD591
NM_152389CCDC1081
NM_173632ZNF7761
NM_0011052051
NM_0011052041
NM_0011052031
NM_014328RUSC11
NM_182697UBE2H1
NM_003344UBE2H1
NM_015458MTMR91
NM_207407TMPRSS11F1
NM_0152411
XM_001128811LOC7312101
XM_933935LOC6467781
XM_943239LOC6467781
NM_020647JPH11
NM_181079IL21R1
NM_021798IL21R1
NM_181078IL21R1
NM_003643GCM11
NM_033170B3GALT51
NM_033173B3GALT51
NM_033171B3GALT51
NM_006057B3GALT51
NM_033172B3GALT51
NM_004383CSK1
NM_020820PREX11
NM_198492CLEC4G1
NM_001082959SCARB11
NM_005505SCARB11
XM_001130364LOC7284171
XM_001130184LOC7308431
NM_170708LMNA1
NM_170707LMNA1
NM_000088COL1A11
NM_001080441LOC1439411
XM_940353LOC1439411
NM_001082480ZNF6231
NM_014789ZNF6231
NM_016575NT5DC31
NM_017728TMEM1041
NM_004176SREBF11
NM_001005291SREBF11
NM_004914RAB361
NM_004514FOXK21
XM_001134363FOXK21
XM_001134364FOXK21
NM_177967UBAC21
NM_014405CACNG41
NM_013382POMT21
NM_007103NDUFV11
NM_006927ST3GAL21
NM_021149COTL11
NM_001694ATP6V0C1
XM_001130742ATP6V0C1
NM_020128MDM11
NM_182923KLC11
NM_000596IGFBP11
NM_080836STK351
NM_0011055201
NM_001039547GK51
NM_001026213CYP11B11
NM_000497CYP11B11
NM_001419ELAVL11
NM_183337RGS111
NM_003834RGS111
NM_024942C10orf881
NM_152482C19orf251
NM_003648DGKD1
NM_152879DGKD1
NM_015079TBC1D2B1
NM_052995CLRN11
XM_001131326LOC7297911
XM_001131187LOC7319001
XM_001131604C6orf2051
NM_001010909C6orf2051
NM_020960GPR1071
NM_020831MKL11
NM_018091ELP31
NM_014718CLSTN31
NM_014704KIAA05621
NM_001662ARF51
NM_000808GABRA31
NM_175736FMNL31
NM_198900FMNL31
NM_002861PCYT21
XM_944850SLC45A41
NM_001080431SLC45A41
NM_015074KIF1B1
NM_024626VTCN11
NM_170600SH2D3C1
NM_001083603PTCH11
NM_001083607PTCH11
NM_001083602PTCH11
NM_001083605PTCH11
NM_001083606PTCH11
NM_001083604PTCH11
NM_000264PTCH11
NM_014030GIT11
NM_0010854541
NM_023946LYNX11
NM_177458LYNX11
NM_032853MUM11
NM_024894NOL101
NM_007261CD300A1
NM_152511DUSP181
NM_032283ZDHHC181
NM_002143HPCA1
NM_017596KIF21B1
NM_020639RIPK41
NM_005883APC21
NM_058243BRD41
NM_0011046471
NM_018155SLC25A361
NM_031432UCK11
NM_001044370MPPED11
NM_014240LIMD11
NM_007033RER11
NM_0208831
XM_379273FLJ141861
NM_019106SEPT31
NM_015184PLCL21
NM_001001795MGC708571
NM_152906C22orf251
NM_021905GABBR11
NM_021904GABBR11
NM_021903GABBR11
NM_001470GABBR11
NM_138736GNAO11
NM_181521CMTM41
NM_207012AP3M11
NM_012095AP3M11
NM_130830LRRC151
NM_020148SPIRE11
NM_015266SLC9A81
NM_005895GOLGA31
NM_004745DLGAP21
NM_001002254DGAT2L41
NM_005425TNP21
NM_001004303C1orf1681
NM_181502SPINLW11
NM_020398SPINLW11
NM_013305ST8SIA51
NM_001933DLST1
NM_020310MNT1
NM_003253TIAM11
NM_014023WDR371
NM_005806OLIG21
NM_004657SDPR1
NM_024871MAP6D11
NM_194457UBE2J21
NM_194315UBE2J21
NM_058167UBE2J21
NM_194458UBE2J21
NM_015155LARP51
NM_003714STC21
NM_018117BRWD21
NM_005969NAP1L41
NM_014588VSX11
NM_000437PAFAH21
NM_001024455RGAG41
NM_014979SV2C1
XM_001132013ANKH1
NM_001083621ZBTB401
NM_014870ZBTB401
NM_019109ALG11
NM_001039618CREBZF1
NM_015077SARM11
NM_005430WNT11
NM_138428C1orf2121
NM_003576STK241
NM_001032296STK241
NM_015557CHD51

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