Predicted Off-targets for siRNA "gccgagaucgcacagagacuu" 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

2 hits were found for CGAGAUCGCACAGAGACUU (0 guide strand hits and 2 sense strand hits.)

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_144769 FOXI1 1912 1930 ggGUCUCUGUGuGAUCUCu47 4 9   false   <90%   2011
NM_012188 FOXI1 2197 2215 ggGUCUCUGUGuGAUCUCu47 4 9   false   <90%   2296


3 prime UTR Seed matches

Hits to same gene : 0
Hits to other genes : 539
View matched accessions

3 prime seed match details

AccessionGene nameHits to this gene
NM_177538CYP20A14
NM_021167GATAD13
NM_018177N4BP22
NM_005044PRKX2
NM_024607PPP1R3B2
NM_001040441ZBTB82
XM_001124597LOC7304112
NM_002061GCLM2
NM_007047BTN3A22
NM_015375RIPK52
NM_199462RIPK52
NM_001030288SPN2
NM_003123SPN2
NM_001908CTSB2
NM_147781CTSB2
NM_147783CTSB2
NM_147780CTSB2
NM_147782CTSB2
NM_001077196PDE11A2
NM_001077197PDE11A2
NM_016953PDE11A2
NM_002716PPP2R1B2
NM_0010996782
NM_024561NARG1L2
NM_014994MAPKBP12
XM_943571LOC6469162
NM_015074KIF1B2
NM_018712ELMOD12
NM_004804CIAO12
NM_022470ZMAT32
NM_152240ZMAT32
NM_198549FAM73A2
NM_022777RABL52
NM_181705LYRM72
NM_052928SMYD42
NM_0152972
XM_942240LOC6505572
NM_019046ANKRD161
NM_177972TUB1
NM_003320TUB1
NM_138454TXNL61
NM_001031681CTNS1
NM_004937CTNS1
NM_022353OSGEPL11
NM_003810TNFSF101
NM_052926PNMA51
NM_0011031511
NM_0011031501
NM_006814PSMF11
NM_178578PSMF11
NM_022497MRPS251
NM_005565LCP21
NM_013345GPR1321
NM_148912ABHD111
NM_172014TNFSF141
NM_003807TNFSF141
NM_019079L1TD11
NM_015666GTPBP51
NM_016422RNF1411
NM_014089NUPL11
NM_001008564NUPL11
NM_207672GRIPAP11
NM_033220TRIM141
NM_003763STX161
NM_001001433STX161
XM_001131704LOC7299001
NM_152636METT5D11
NM_001024947YIPF51
NM_030799YIPF51
NM_001013649LOC3889691
NM_021994ZNF277P1
NM_005347HSPA51
NM_024963FBXL181
NM_182578THEM51
NM_018085IPO91
NM_174902LDLRAD31
NM_017656ZNF5621
NM_012290TLK11
NM_000671ADH51
XM_001128649LOC7288901
XM_001125920LOC7278561
XM_376814MGC130051
NM_139158ALS2CR71
NM_001042584CD1E1
NM_001042586CD1E1
NM_030893CD1E1
NM_001042587CD1E1
NM_001042585CD1E1
NM_001042583CD1E1
XM_001128800LOC7283511
XM_001130904LOC7309591
NM_015629PRPF311
NM_017946FKBP141
NM_138393REEP61
NM_005128DOPEY21
NM_016562TLR71
NM_003430ZNF911
NM_148903GREB11
NM_000849GSTM31
NM_032788ZNF5141
NM_024902FLJ132361
NM_001024215FBLIM11
NM_022112P53AIP11
NM_138368DKFZp761E1981
NM_0011003891
NM_152496MANEAL1
NM_001066TNFRSF1B1
NM_017861PIGX1
XM_379378LOC4012201
NM_133493CD1091
NM_018438FBXO61
NM_152361EID2B1
NM_000629IFNAR11
NM_018068PIWIL21
NM_198542ZNF7731
NM_002645PIK3C2A1
XM_927226LOC6429211
NM_032102SFRS2B1
NM_024627C22orf291
NM_014898ZFP301
XM_001132728LOC7323141
XM_001128520LOC7287991
NM_014293NPTXR1
NM_024313NOL121
NM_018941CLN81
NM_015453THUMPD31
NM_015264C22orf91
NM_001009880C22orf91
NM_007011ABHD21
NM_152924ABHD21
NM_152396METTL61
NM_015151DIP2A1
NM_032121DKFZp564K1421
NM_002439MSH31
NM_144582TEX2611
NM_006969ZNF281
NM_033274ADAM191
NM_170601SIAE1
NM_030671PTPRO1
NM_030670PTPRO1
NM_153212GJB41
NM_001928CFD1
NM_001939DRP21
NM_022568ALDH8A11
NM_170771ALDH8A11
NM_207351PRRT31
XM_001131164LOC7309711
NM_198887NUP431
NM_0216231
NM_002853RAD11
NM_133377RAD11
NM_014331SLC7A111
NM_032433ZNF3331
NM_152531C3orf211
NM_025061LRRC8E1
NM_144721THAP61
NM_012317LDOC11
NM_053044HTRA31
NM_152913TMEM1301
NM_017856GEMIN81
NM_001042479GEMIN81
NM_001042480GEMIN81
NM_178128FADS61
NM_017614BHMT21
NM_002579PALM1
NM_001040134PALM1
XM_933539MGC30321
XM_944529MGC30321
NM_004331BNIP3L1
NM_004861GAL3ST11
NM_006852TLK21
NM_0011127071
NM_207521RTN41
NM_153828RTN41
NM_020532RTN41
NM_007008RTN41
NM_207520RTN41
NM_032869NUDCD11
NM_005417SRC1
NM_198291SRC1
XM_001128437LOC7281341
XM_001128309LOC7306631
NM_001512GSTA41
NM_172247CSF2RA1
NM_172249CSF2RA1
NM_001031710KLHL71
NM_018846KLHL71
NM_000136FANCC1
XM_927706LOC6445911
NM_153369KIAA19191
NM_003929RAB7L11
NM_001079529LOC2021341
NM_001031679MSRB31
NM_198080MSRB31
NM_006197PCM11
NM_019099C1orf1831
NM_198926C1orf1831
NM_178324SPTLC11
NM_001037165FOXK11
NM_198179GPR1031
NM_147192DMBX11
NM_172225DMBX11
NM_003417ZNF2641
NM_018292QRSL11
NM_138801GALM1
NM_001455FOXO3A1
NM_201559FOXO3A1
NM_0208551
XM_001126195LOC7279421
NM_024733ZNF6651
NM_153260LRRC571
NM_001040025ARL161
NM_080758TBX61
NM_014033METTL7A1
NM_015173TBC1D11
NM_0010937551
NM_0010937561
NM_024941FLJ136111
NM_024750LRRC21
NM_024512LRRC21
NM_014883FAM13A11
NM_001015045FAM13A11
NM_023928AACS1
NM_000227LAMA31
NM_198129LAMA31
NM_153717EVC1
NM_013322SNX101
NM_006670TPBG1
NM_014741KIAA06521
NM_001039960SLC4A81
NM_001002034FAM109B1
NM_001080484KIAA17511
XM_936307KIAA17511
NM_020738KIDINS2201
NM_197970BOLL1
NM_033030BOLL1
NM_198213OASL1
NM_006278ST3GAL41
NM_005766FARP11
NM_024909C6orf1341
NM_001008493ENAH1
NM_018212ENAH1
NM_000934SERPINF21
NM_0150381
NM_001081491NXF11
NM_012218ILF31
NM_024103SLC25A231
NM_000527LDLR1
NM_152903KBTBD61
NM_002546TNFRSF11B1
NM_012425RSU11
NM_152724RSU11
NM_080591PTGS11
NM_000962PTGS11
NM_052858MARVELD31
NM_001012339DNAJA51
NM_194283DNAJA51
XM_498578C14orf821
XM_944991C14orf821
NM_020822KCNT11
NM_015488PNKD1
NM_022572PNKD1
NM_006167NKX3-11
NM_001012508SPRN1
NM_018000MREG1
NM_145207SPATA51
NM_024541C10orf761
NM_006011ST8SIA21
NM_022041GAN1
NM_017523XAF11
NM_199139XAF11
NM_001024380TM2D21
NM_078473TM2D21
NM_001024381TM2D21
NM_031940TM2D21
NM_206538LOC2843611
NM_175063LOC2843611
NM_006321ARIH21
NM_001002026CLDN181
NM_016369CLDN181
NM_130440PTPRF1
NM_002840PTPRF1
NM_002416CXCL91
NM_203453PPAPDC21
NM_015659RSL1D11
NM_004808NMT21
NM_000821GGCX1
XM_929878LOC6469151
NM_001007525NWD11
NM_002725PRELP1
NM_201348PRELP1
NM_0011025591
NM_0011026511
NM_022048CSNK1G11
NM_174911FAM84B1
NM_022340ZFYVE201
NM_015458MTMR91
NM_013432NFKBIL21
NM_001001420SMAD51
NM_001001419SMAD51
NM_005903SMAD51
XM_001134349LOC7301761
NM_014899RHOBTB31
NM_001039570KREMEN11
NM_001039571KREMEN11
NM_001014342FLG21
NM_152586USP541
NM_024804ZNF6691
NM_133375DIS3L1
NM_198493ANKRD451
NM_016823CRK1
NM_005206CRK1
NM_024345WDR321
XM_001128829LOC6493051
NM_020375C12orf51
NM_000139MS4A21
XM_932529LOC6449491
XM_943887LOC6449491
NM_001040217FAM63A1
NM_001033578SGK31
NM_013257SGK31
NM_170709SGK31
NM_018962DSCR61
NM_013332HIG21
NM_0010987861
NM_001083909GPR1231
NM_032855HSH2D1
NM_007211RASSF81
NM_130446KLHL61
NM_001040450FAM63B1
NM_001040453FAM63B1
NM_003897IER31
NM_001065TNFRSF1A1
NM_052916RNF1571
NM_001204BMPR21
NM_023076C16orf281
NM_005707PDCD71
XM_928252LOC6452121
XM_939117LOC6452121
NM_001077349ZNF6821
NM_033196ZNF6821
NM_025257SLC44A41
NM_144775SMCR81
NM_015431TRIM581
NM_018124RFWD31
NM_153687IKIP1
NM_001014283DCUN1D21
NM_018141MRPS101
NM_001040701FUT61
NM_000150FUT61
NM_024798SNX221
NM_032374C14orf1531
NM_005975PTK61
NM_002985CCL51
NM_016261TUBD11
NM_030626LRRC271
NM_133444ZNF5261
NM_144687NLRP121
NM_052941GBP41
NM_006166NFYB1
NM_019089HES21
NM_023923PHACTR41
NM_001048183PHACTR41
NM_005497GJA71
NM_001080383GJA71
NM_002203ITGA21
NM_030776ZBP11
XM_938924LOC6440921
XM_001130314LOC6440921
NM_016433GLTP1
NM_005895GOLGA31
NM_001992F2R1
NM_020825CRAMP1L1
XM_934649C1orf341
XM_945958C1orf341
XM_001132013ANKH1
NM_054027ANKH1
NM_001039547GK51
NM_0011045861
NM_024744ALS2CR81
NM_145039MGC163851
NM_032898C3orf341
NM_001638APOF1
NM_144597C15orf401
NM_025059C6orf971
NM_018324OLAH1
NM_001039702OLAH1
NM_000500CYP21A21
NM_001012986LOC3889101
NM_001277CHKA1
NM_212469CHKA1
NM_203418DSCR11
NM_203417DSCR11
NM_004414DSCR11
NM_018656SLC35E31
NM_052884SIGLEC111
NM_006464TGOLN21
NM_207322NLF11
XM_001134379LOC7323501
XM_001128421LOC7280691
NM_152529GPR1551
NM_001033045GPR1551
NM_001076675ZNF6261
NM_003082SNAPC11
NM_003774GALNT41
NM_138706B3GNT61
NM_001083625ANKRD121
NM_015208ANKRD121
NM_006455SC651
NM_138572TBN1
NM_001001349NKIRAS21
NM_017595NKIRAS21
NM_0010996941
NM_145060C18orf241
NM_001039535C18orf241
NM_014186COMMD91
NM_0011016531
NM_020704FAM40B1
NM_182594ZNF4541
NM_017765PQLC21
NM_001040126PQLC21
NM_001040125PQLC21
NM_173811C11orf771
NM_024311MFSD111
NM_005793NME61
NM_181712ANKRD381
NM_031409CCR61
NM_004367CCR61
NM_0010988191
NM_0010988181
NM_000923PDE4C1
NM_000990RPL27A1
NM_207320OTUD6A1
NM_007107SSR31
NM_001001561GGA11
NM_005603ATP8B11
NM_030980ISG20L21
NM_015064ERC11
NM_178039ERC11
NM_178040ERC11
NM_178038ERC11
NM_178037ERC11
NM_001031740MANEAL1
NM_022067C14orf1331
NM_003685KHSRP1
NM_000833GRIN2A1
NM_003979GPRC5A1
NM_001005473PLCXD31
NM_003970MYOM21
NM_002676PMM11
NM_001024460VNN31
NM_078625VNN31
NM_018399VNN31
XM_001134327LOC7323241
XM_001134208LOC7299751
NM_021979HSPA21
NM_014948UBOX51
NM_199415UBOX51
NM_001031727MGC32071
NM_032285MGC32071
NM_001037582SCD51
XM_930750LOC6423661
XM_943652LOC6423661
NM_005133RCE11
NM_001032279RCE11
NM_000148FUT11
NM_005488TOM11
NM_016169SUFU1
NM_001034852SMOC11
NM_022137SMOC11
NM_005446P2RXL11
NM_001296CCBP21
NM_001167BIRC41
XM_001129103LOC7290291
XM_001128912LOC7312381
XM_940069PPP1R3E1
XM_927029PPP1R3E1
NM_014240LIMD11
NM_004866SCAMP11
XM_001129732FLJ226591
XM_001133602LOC3884361
NM_152253CHKB1
NM_152247CPT1B1
NM_001646APOC41
NM_002711PPP1R3A1
NM_018032LUC7L1
XM_938374LOC6440101
NM_024756MMRN21
XM_001131234LOC7303381
XM_001126530LOC7305481
NM_183413FBXO441
NM_033182FBXO441
NM_001014765FBXO441
NM_183412FBXO441
NM_033550TP53RK1
NM_014442SIGLEC81
NM_015328KIAA08281
NM_020914RNF2131
NM_152569C9orf661
NM_0011126631
NM_006629ZNF2711
NM_003462DNALI11
NM_0149871
NM_015329KIAA08921
NM_017748CCDC491
NM_152290C1orf1581
NM_194317LYPD61
NM_152757FLJ303131
NM_018036C14orf1031
NM_007249KLF121
NM_018639WSB21
NM_015144ZCCHC141
NM_016339RAPGEFL11
NM_000084CLCN51
NM_030929KAZALD11
NM_001018067SERBP11
NM_015640SERBP11
NM_001018069SERBP11
NM_001018068SERBP11
NM_022912REEP11
NM_001001502SNCB1
NM_003085SNCB1
NM_0207221
NM_032900ARHGAP191
NM_020975RET1
NM_005986SOX11
NM_018096NLE11
NM_001014445NLE11
NM_004285H6PD1
XM_937358LOC6423841
XM_926149LOC6423841
NM_014484MOCS31
NM_016426GTSE11
NM_003221TFAP2B1
NM_006505PVR1
NM_018454NUSAP11
NM_016359NUSAP11
XM_060535LOC1275451
XM_940692LOC1275451

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