Predicted Off-targets for siRNA "ucuccgcgaggacugggga" 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

16 hits were found for UCUCCGCGAGGACUGGGGA (5 guide strand hits and 11 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
XM_939240 LOC389813 1995 2013 cCgCCGCGAGGACUGGGac70 4 14 c false   <90%   2832
NM_001080482 LOC389813 1995 2013 cCgCCGCGAGGACUGGGac70 4 14 c false   <90%   2832
NM_152856 RBM10 2315 2333 cCUCCGCGAGGACUGGuGg69 3 15 ac false   <90%   3190
NM_005676 RBM10 2549 2567 cCUCCGCGAGGACUGGuGg69 3 15 ac false   <90%   3415
NM_031917 ANGPTL6 1233 1251 UCUCCugGAGGACUGGGGg-34 3 11 bc false   <90%   1857


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_001037343 CDKL5 1668 1686 UCCCCAGUCCUCuaGGAGu65 3 12   false   <90%   3430
NM_003159 CDKL5 1672 1690 UCCCCAGUCCUCuaGGAGu65 3 12   false   <90%   3434
NM_015432 PLEKHG4 1178 1196 UCCCCAGUCCUCaCGGcaA63 3 12   false   <90%   6826
NM_182539 MGC33600 1043 1061 caCCCAGUCCUCGaGGAGc62 4 11 c false   <90%   1662
NM_001079804 GAA 239 257 UCCCCAGUCCUgGaGGAGA46 2 11   false   <90%   3517
NM_001079803 GAA 319 337 UCCCCAGUCCUgGaGGAGA46 2 11   false   <90%   3597
NM_000152 GAA 504 522 UCCCCAGUCCUgGaGGAGA46 2 11   false   <90%   3782
XM_944606 LOC646482 688 706 gCCCCAGgCCUCGCGGAGc30 3 10 bc false   <90%   1674
XM_933644 LOC646482 688 706 gCCCCAGgCCUCGCGGAGc30 3 10 bc false   <90%   1674
XM_944973 LOC651842 692 710 gCCCCAGgCCUCGCGGAac28 4 9 c false   <90%   960
XM_931742 LOC643678 692 710 gCCCCAGgCCUCGCGGAac28 4 9 c false   <90%   960


3 prime UTR Seed matches

Hits to same gene : 0
Hits to other genes : 577
View matched accessions

3 prime seed match details

AccessionGene nameHits to this gene
NM_019089HES23
NM_015284KIAA04672
NM_004285H6PD2
NM_182487OLFML2A2
NM_001017989OPA32
NM_000278PAX22
NM_003989PAX22
NM_003990PAX22
NM_003987PAX22
NM_003988PAX22
NM_178129P2RY82
NM_014826CDC42BPA2
NM_003607CDC42BPA2
NM_001003698RREB12
NM_001003699RREB12
NM_002955RREB12
NM_006651CPLX12
NM_002501NFIX2
NM_032538TTBK12
XM_001131828BBS52
XM_001131846BBS52
NM_152384BBS52
XM_379029LOC4008792
NM_001017916CYB5612
NM_001915CYB5612
NM_001017917CYB5612
NM_018028SAMD4B2
XM_001134172LOC7300342
XM_001133186LOC7313452
XM_001134398LOC7302562
XM_930678LOC6424412
XM_001134399LOC7302572
NM_144661C10orf821
XM_001127675LOC7285301
XM_001128953LOC7312491
NM_001011703FAM125B1
NM_001008566TPST21
NM_003595TPST21
NM_0146871
NM_176823S100A7A1
NM_004155SERPINB91
NM_207334FAM43B1
XM_939520LOC4410501
NM_022082C20orf591
NM_000276OCRL1
NM_001587OCRL1
NM_052840BRUNOL61
NM_006052DSCR31
NM_033225CSMD11
NM_006857RY11
NM_206909PSD31
NM_015310PSD31
NM_080706TRPV11
NM_018727TRPV11
NM_080704TRPV11
NM_080705TRPV11
NM_001010862SPIN31
NM_005933MLL1
NM_020465NDRG41
NM_022910NDRG41
NM_0010997841
NM_005400PRKCE1
NM_001116ADCY91
NM_006288THY11
NM_007185TNRC41
NM_020421ADCK11
NM_005216DDOST1
NM_003492TMEM1871
NM_022783DEPDC61
NM_001040020FAM3C1
NM_014888FAM3C1
NM_001083314CHMP1A1
NM_002768CHMP1A1
NM_003558PIP5K1B1
NM_020825CRAMP1L1
NM_001013661VSIG81
NM_182557BCL9L1
NM_006142SFN1
NM_014023WDR371
NM_003957BRSK21
NM_080797DIDO11
NM_017723C9orf1671
NM_145012CCNY1
NM_024817THSD41
NM_001001791C10orf551
NM_006257PRKCQ1
NM_015069ZNF4231
NM_001949E2F31
XM_001132864HIP1R1
NM_003959HIP1R1
NM_177403RAB7B1
NM_145321OSBPL31
NM_145320OSBPL31
NM_145322OSBPL31
NM_015550OSBPL31
NM_0010992701
XM_938741LOC1164121
XM_375665LOC1164121
NM_016185HN11
NM_001002032HN11
NM_001002033HN11
NM_017433MYO3A1
XM_499022LOC4411241
XM_001129100LOC7290281
XM_930755LOC6530561
XM_001130184LOC7308431
XM_001130364LOC7284171
XM_379273FLJ141861
XM_933614LOC6464341
NM_002990CCL221
XM_931612LOC6435291
XM_943256LOC6435291
XM_001128973LOC7284491
NM_006845KIF2C1
XM_001132246LOC7299971
NM_206926SEPN11
NM_020451SEPN11
NM_001008701LPHN11
NM_014921LPHN11
NM_015227POFUT21
NM_017712PGPEP11
NM_022468MMP251
NM_024640YRDC1
NM_172000TEDDM11
XM_001134027LOC7318891
XM_001134374LOC7301321
NM_004399DDX111
NM_030653DDX111
NM_152438DDX111
NM_018711SVOP1
NM_033226ABCC121
NM_021192HOXD111
XM_927238LOC6439881
XM_936418LOC6473471
NM_000859HMGCR1
NM_019596C21orf621
XM_941352LOC2552751
XM_171855LOC2552751
NM_182705FAM101B1
XM_001126665FAM101B1
NM_022832USP461
NM_057174PEX161
XM_941994TMEM132C1
XM_044062TMEM132C1
XM_944900LOC6437701
XM_931792LOC6437701
NM_001048209HNT1
NM_016522HNT1
NM_017553INOC11
NM_003751EIF3S91
NM_001037283EIF3S91
NM_032807FBXO181
NM_178150FBXO181
NM_0011101991
NM_015896ZMYND101
NM_014631SH3PXD2A1
NM_002984CCL41
NM_207007CCL4L21
NM_001001435CCL4L11
XM_001133190LOC7288351
XM_001133183LOC7288351
XM_001125732LOC7304241
XM_001125707LOC7304241
XM_001125761LOC7304241
XM_001133187LOC7288351
NM_183361DTNB1
NM_021907DTNB1
NM_033147DTNB1
NM_033148DTNB1
NM_183360DTNB1
NM_138793CANT11
NM_021260ZFYVE11
NM_178441ZFYVE11
NM_001014447CPZ1
NM_001014448CPZ1
NM_003652CPZ1
NM_006096NDRG11
NM_001876CPT1A1
NM_152371C1orf931
NM_016621PHF21A1
NM_0011018021
NM_000168GLI31
NM_004567PFKFB41
NM_145253FAM100A1
NM_002189IL15RA1
NM_172200IL15RA1
NM_018027FRMD4A1
NM_052925LENG81
NM_005086SSPN1
NM_001383DPH11
NM_031858NBR11
NM_031862NBR11
NM_005899NBR11
XM_001124828LOC7277321
XM_001124651LOC7277321
NM_018384GIMAP51
NM_020899ZBTB41
NM_058243BRD41
NM_017991FLJ100811
NM_152686DNAJC181
NM_203404AMPD21
NM_139156AMPD21
NM_004037AMPD21
NM_000358TGFBI1
NM_006045ATP9A1
NM_007322RANBP31
NM_003624RANBP31
NM_152705POLR1D1
XM_001130526LOC7286361
XM_001130555LOC7286361
XM_001130543LOC7286361
XM_001130536LOC7286361
NM_031475ESPN1
NM_016060MED311
NM_001040710FLJ308511
XM_001127419FLJ308511
XM_001130207FLJ308511
NM_007079PTP4A31
NM_032611PTP4A31
NM_001080530LOC920171
NM_020477ANK11
NM_020475ANK11
NM_000037ANK11
NM_020476ANK11
NM_020478ANK11
NM_020480ANK11
NM_014732KIAA05131
NM_207401FLJ457171
NM_014909VASH11
NM_170708LMNA1
NM_170707LMNA1
NM_019044CCDC931
NM_153256C10orf471
NM_002347LY6H1
NM_012181FKBP81
NM_207511C9orf1391
NM_003088FSCN11
NM_004171SLC1A21
NM_018999KIAA11281
NM_015666GTPBP51
NM_020199C5orf151
NM_000102CYP17A11
NM_198843SFTPB1
NM_0153061
NM_001082959SCARB11
NM_005505SCARB11
NM_031215CABLES21
NM_080833C20orf1511
NM_173541C10orf911
NM_0207331
NM_001081563DMPK1
NM_004409DMPK1
NM_001081560DMPK1
NM_001081562DMPK1
NM_000221KHK1
NM_006488KHK1
NM_017790RGS31
NM_0071501
NM_003153STAT61
NM_022574PERQ11
NM_001029939ZFAT11
NM_001114ADCY71
NM_003224ARFRP11
NM_0011096891
NM_021061ZNF2501
NM_138401FAM125A1
NM_015553PIP3-E1
NM_021025TLX31
NM_020836KIAA14461
NM_006553SLMO11
NM_015063SLC8A21
NM_007350PHLDA11
NM_153631HOXA31
NM_153632HOXA31
NM_030661HOXA31
XM_001132233LOC7300531
NM_005098MSC1
NM_005984SLC25A11
NM_003899ARHGEF71
NM_080539COLQ1
NM_080538COLQ1
NM_080544COLQ1
NM_005677COLQ1
NM_080541COLQ1
NM_181798KCNQ11
NM_000218KCNQ11
NM_005354JUND1
NM_030802FAM117A1
NM_001037165FOXK11
NM_001013690LOC4017201
NM_182528C1QL21
XM_001133002LOC7288041
XM_933935LOC6467781
XM_943239LOC6467781
XM_498841LOC4407481
XM_937862LOC6449621
NM_004308ARHGAP11
NM_032323TMEM791
NM_178564NRBP21
NM_001007279RASL10A1
NM_006477RASL10A1
NM_006014LAGE31
XM_940825DLGAP31
NM_001080418DLGAP31
NM_013301CCDC1061
NM_004588SCN2B1
NM_005342HMGB31
NM_198392TCF211
NM_001042402ASAHL1
NM_201397GPX11
NM_016269LEF11
NM_002115HK31
NM_030957ADAMTS101
NM_020708SLC12A51
NM_004749TBRG41
NM_030900TBRG41
NM_199122TBRG41
NM_022134GAL3ST21
XM_940609FLJ250761
XM_059689FLJ250761
NM_017623CNNM31
NM_199078CNNM31
NM_015722DRD1IP1
NM_015002FBXO211
NM_033624FBXO211
NM_003099SNX11
NM_152826SNX11
NM_148955SNX11
NM_003575ZNF2821
NM_0010986321
NM_032375AKT1S11
NM_0010986331
NM_133374ZNF6181
NM_0010937251
NM_014911AAK11
NM_018045BSDC11
NM_005338HIP11
NM_0010987211
NM_0010987221
NM_004485GNG41
NM_005435ARHGEF51
NM_033386MICALL11
NM_017924C14orf1191
NM_002349LY751
NM_0011055701
NM_004481GALNT21
XM_001126066LOC7304971
NM_172247CSF2RA1
NM_172249CSF2RA1
NM_006140CSF2RA1
NM_172245CSF2RA1
NM_033310KCNK41
NM_005207CRKL1
NM_018189DPPA41
NM_004696SLC16A41
NM_001002836ZNF7871
NM_005291GPR171
NM_022048CSNK1G11
XM_928029RNF1871
XM_001129309RNF1871
NM_205843NFIC1
NM_005597NFIC1
XM_001131943LOC7299791
XM_001128763LOC7311881
NM_002883RANGAP11
NM_032752ZNF4961
NM_001029864KIAA17551
NM_014675CROCC1
NM_173065IL28RA1
NM_173064IL28RA1
NM_170743IL28RA1
NM_018111FLJ104901
NM_032508TMEM185A1
NM_014880CD3021
NM_000784CYP27A11
NM_017904TTC221
NM_000054AVPR21
NM_004332BPHL1
NM_005935AFF11
XM_001130170LOC7292751
XM_001127723LOC7308781
NM_020851ISLR21
NM_032880IGSF211
NM_004269CRSP81
NM_018649H2AFY21
NM_198545C1orf1871
NM_015253WSCD11
XM_001133004LOC7288091
NM_138983OLIG11
NM_005187CBFA2T31
NM_175931CBFA2T31
NM_000118ENG1
NM_032294CAMKK11
NM_172206CAMKK11
XM_927936LOC6448411
XM_935685LOC6419331
XM_938176LOC6448411
NM_003714STC21
NM_005934MLLT11
NM_001005209MGC998131
NM_000742CHRNA21
NM_198552FAM89A1
NM_005430WNT11
NM_001761CCNF1
NM_023076C16orf281
NM_030651PRRT11
NM_031891CDH201
NM_033131WNT3A1
XM_926711LOC6433821
XM_939770LOC6506831
NM_174911FAM84B1
NM_002199IRF21
NM_001077446TSEN341
NM_024075TSEN341
NM_138390TMEM1691
NM_018036C14orf1031
NM_001616ACVR2A1
NM_018717MAML31
NM_052896CSMD21
NM_020151STARD71
NM_023080C8orf331
NM_198427BCAN1
NM_182612PDDC11
XM_001131270LOC7309901
NM_024701ASB131
NM_023067FOXL21
NM_001080457LRRC4B1
XM_936789LRRC4B1
NM_006160NEUROD21
NM_022350LRAP1
NM_017523XAF11
NM_199139XAF11
NM_014898ZFP301
NM_020742NLGN4X1
NM_181332NLGN4X1
NM_0208271
NM_004776B4GALT51
NM_014435ASAHL1
NM_023075MPPE11
NM_153029N4BP11
NM_198081SCML41
NM_002730PRKACA1
NM_207518PRKACA1
NM_005491CXorf61
NM_198849LOC2835141
NM_138362FAM104B1
NM_176877INADL1
NM_001006638RAB371
NM_014924KIAA08311
NM_014033METTL7A1
NM_022787NMNAT11
NM_004051BDH11
NM_203315BDH11
NM_203314BDH11
NM_001004302ZNF7831
NM_007347AP4E11
NM_001013655LOC3898341
XM_001125792LOC7278341
XM_926013LOC6423981
NM_005895GOLGA31
NM_0207211
NM_001017396ZNF21
NM_021088ZNF21
XM_940089FLJ396391
XM_370932FLJ396391
NM_181489ZNF4451
NM_003023SH3BP21
NM_001296CCBP21
XM_001126091LOC7304961
NM_021079NMT11
NM_020318PAPPA21
NM_015101GLT25D21
NM_014405CACNG41
NM_138468ICA1L1
NM_002088GRIK51
NM_014002IKBKE1
NM_153334SCARF21
NM_182895SCARF21
NM_004976KCNC11
NM_001031617COX191
NM_021925C2orf431
NM_024866ADM21
NM_007371BRD31
NM_145298APOBEC3F1
NM_031491RBP51
NM_024507KREMEN21
NM_014762DHCR241
NM_002917RFNG1
XM_001132711RFNG1
XM_941762SETD1B1
XM_037523SETD1B1
NM_004488GP51
NM_176806MOCS21
NM_178502DTX31
NM_003918GYG21
NM_001079855GYG21
NM_002861PCYT21
NM_002698POU2F21
NM_130830LRRC151
NM_003598TEAD21
NM_024644C14orf1691
NM_018440PAG11
NM_018969GPR1731
NM_015075IQSEC21
NM_0011111251
NM_018941CLN81
NM_203403C9orf1501
NM_002577PAK21
NM_001008530LGMN1
NM_005606LGMN1
XM_945019LOC6434411
XM_933124LOC6434411
XM_931281LOC6430721
XM_943769LOC6430721
NM_0011099741
NM_014309RBM91
NM_001082576RBM91
NM_001082577RBM91
NM_001031695RBM91
NM_001082578RBM91
NM_001082579RBM91
XM_943323LOC6467191
XM_933842LOC6467191
NM_023110FGFR11
NM_023106FGFR11
NM_015850FGFR11
NM_023111FGFR11
NM_023105FGFR11
NM_002911UPF11
NM_003908EIF2S21
NM_016196RBM191
XM_001134334RBM191
NM_014744TBC1D51
NM_022497MRPS251
NM_001030005CPLX31
NM_014360NKX2-81
NM_032728PPAPDC31
NM_002359MAFG1
NM_032711MAFG1
NM_183337RGS111
NM_003834RGS111
NM_178172LOC3383281
NM_001032363C1orf1511
NM_001419ELAVL11
NM_004892SEC22B1
NM_015166MLC11
NM_139202MLC11
NM_006950SYN11
NM_133499SYN11
NM_014978SORCS31
NM_024527ABHD81
NM_004455EXTL11
NM_002196INSM11
NM_015995KLF131
NM_024085ATG9A1
NM_001077198ATG9A1
NM_020877DNAH21
NM_006555YKT61
NM_198389PDPN1
NM_006474PDPN1
NM_001006624PDPN1
NM_001006625PDPN1
NM_001033667LY91
NM_001039517C1orf1041
NM_006167NKX3-11
NM_014400LYPD31
NM_201266NRP21
NM_003872NRP21
NM_201279NRP21
NM_020179C11orf751
NM_001018003SORBS31
NM_005775SORBS31
NM_018371ChGn1
NM_017410HOXC131
NM_176096CDK5RAP31
NM_020792AADACL11
NM_018715RCC21

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