Predicted Off-targets for siRNA "augcgccagcuaaaaccaa" 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 AUGCGCCAGCUAAAACCAA (2 guide strand hits and 5 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_014709 USP34 3191 3209 AUGCcCCAGCUAAAACCug40 3 12 c false   <90%   11326
NM_021018 HIST1H3F 428 446 gUGCGCCAaCUuAAACCAA4 3 7   false   <90%   466


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_001129251 HEG1 4960 4978 UUGGUUUUAGCUGGaGgcU49 3 14 c false   <90%   9136
XM_087386 HEG1 5038 5056 UUGGUUUUAGCUGGaGgcU49 3 14 c false   <90%   9213
NM_001037175 SUSD4 213 231 gUGGUUUcAGCUGGCGCug28 4 9 c false   <90%   1044
NM_017982 SUSD4 213 231 gUGGUUUcAGCUGGCGCug28 4 9 c false   <90%   2966
NM_006796 AFG3L2 2544 2562 gUGGUUUcAGCUGGuGCAU11 3 6 c false   <90%   2963


3 prime UTR Seed matches

Hits to same gene : 0
Hits to other genes : 347
View matched accessions

3 prime seed match details

AccessionGene nameHits to this gene
NM_020951ZNF5292
NM_021574BCR2
NM_004327BCR2
NM_006237POU4F11
NM_173602DIP2B1
NM_0153481
NM_030952NUAK21
XM_941684LOC2204331
XM_930211LOC2204331
NM_005332HBZ1
XM_943313LOC6484051
NM_0011025761
NM_153478CSAG11
NM_021912GABRB31
NM_000814GABRB31
NM_205848SYT61
NM_006301MAP3K121
NM_015353KCTD21
NM_198581ZC3H61
NM_0321731
NM_001079512LOC7807761
NM_003034ST8SIA11
NM_004571PKNOX11
NM_206914FAM119B1
NM_015433FAM119B1
NM_001008493ENAH1
NM_018212ENAH1
NM_014316CARHSP11
NM_001042476CARHSP11
NM_181705LYRM71
NM_0011096891
NM_021061ZNF2501
XM_001130815LOC6478591
XM_001127102LOC6478591
NM_001039709CBFA2T21
NM_001032999CBFA2T21
NM_005093CBFA2T21
NM_012192FXC11
NM_172037RDH101
NM_014877HELZ1
NM_182493MLCK1
NM_024037C1orf1351
NM_152624DCP21
NM_017831RNF1251
XM_001125918LOC7278721
NM_020714ZNF4901
NM_005955MTF11
NM_001039569AP1S31
NM_003681PDXK1
NM_152458ZNF7851
NM_182686KIAA0319L1
NM_1523571
NM_152455ZSCAN291
NM_001031727MGC32071
NM_032285MGC32071
NM_014157CCDC1131
NM_003203C2orf31
NM_018947CYCS1
NM_006628ARPP-191
NM_001012756ZNF2601
NM_001003795GTF2IRD2B1
NM_005419STAT21
NM_022753S100PBP1
NM_001077619LOC1378861
NM_000761CYP1A21
NM_014056HIGD1A1
NM_0010996681
NM_0010996691
NM_001012659ARGFX1
NM_021625TRPV41
NM_147204TRPV41
XM_001134338LOC7322421
NM_015078MCF2L21
NM_207370GPR1531
NM_012463ATP6V0A21
NM_004067CHN21
NM_001039936CHN21
NM_006749SLC20A21
NM_022468MMP251
NM_006915RP21
NM_014946SPAST1
NM_199436SPAST1
NM_017849TMEM1271
NM_019046ANKRD161
NM_032160DSEL1
NM_018379FAM63A1
NM_033381COL4A51
NM_033380COL4A51
NM_000495COL4A51
NM_014897ZNF6521
NM_207380FLJ433391
NM_032459EFS1
NM_024329EFHD21
NM_012083FRAT21
NM_001201BMP31
NM_002401MAP3K31
NM_203351MAP3K31
NM_003747TNKS1
NM_001032363C1orf1511
NM_001077691ALG91
NM_001077692ALG91
NM_024740ALG91
NM_001077690ALG91
NM_182609ZNF6771
NM_014217KCNK21
NM_001017424KCNK21
NM_001017425KCNK21
NM_005253FOSL21
XM_378973LOC2848011
XM_944897LOC2848011
NM_017455NPTN1
NM_012428NPTN1
NM_025241UBXD11
NM_001002034FAM109B1
NM_032680EFCAB4B1
NM_003091SNRPB1
NM_016346NR2E31
NM_005076CNTN21
NM_058246DNAJB61
NM_015533DAK1
NM_145006SUSD31
XM_209363SIRPB21
XM_939897SIRPB21
NM_152682RWDD4A1
NM_022719DGCR141
NM_015321CRTC11
NM_0010984821
XM_926071LOC6425921
XM_943686SYT71
NM_014030GIT11
NM_0010854541
NM_002699POU3F11
NM_014690FAM131B1
NM_001031690FAM131B1
NM_017623CNNM31
NM_199078CNNM31
XM_495873LOC4400401
XM_941897LOC6524511
NM_001042508LOC6534831
NM_001003674C18orf11
NM_181483C18orf11
NM_181481C18orf11
NM_001003675C18orf11
NM_004338C18orf11
NM_181482C18orf11
NM_134325SLC26A91
NM_052934SLC26A91
NM_030580ZNF341
NM_002997SDC11
NM_001006946SDC11
NM_002376MARK31
NM_003378VGF1
NM_006497HIC11
NM_0010982021
XM_001130722LOC7317691
XM_001127289LOC7283531
XM_001133309LOC7293051
XM_001131633LOC7320241
NM_012306FAIM21
NM_198152UTS2D1
NM_152307C14orf1721
NM_014786ARHGEF171
NM_020731AHRR1
NM_0010988331
NM_0202181
NM_032647CBX21
NM_021135RPS6KA21
NM_001006932RPS6KA21
NM_175609ARFGAP11
NM_018209ARFGAP11
NM_004383CSK1
XM_290799ARHGAP231
NM_002613PDPK11
NM_031268PDPK11
NM_014732KIAA05131
NM_005737ARL4C1
NM_198074OR2C31
NM_001017916CYB5611
NM_001915CYB5611
NM_001017917CYB5611
NM_005835SLC17A21
NM_022489C14orf1731
NM_001031714C14orf1731
NM_020223FAM20C1
NM_003808TNFSF131
NM_172088TNFSF131
NM_172087TNFSF131
NM_172089TNFSF12-TNFSF131
NM_000598IGFBP31
NM_001013398IGFBP31
NM_0010996921
NM_017588WDR51
NM_052821WDR51
NM_176787PIGN1
NM_012327PIGN1
NM_177403RAB7B1
NM_018990CXorf91
NM_003763STX161
NM_001001433STX161
XM_933050LOC3480211
NM_003009SEPW11
NM_000278PAX21
NM_003989PAX21
NM_003990PAX21
NM_003987PAX21
NM_003988PAX21
NM_005226EDG31
XM_378661C17orf511
XM_944416C17orf511
NM_012409PRND1
NM_153718NUP621
NM_012346NUP621
NM_153719NUP621
NM_016553NUP621
NM_001080421UNC13A1
NM_004887CXCL141
NM_017590ZC3H7B1
NM_022872IFI61
NM_002038IFI61
NM_022873IFI61
NM_021067GINS11
NM_0011004181
NM_0011004191
NM_023931ZNF7471
XM_940966LOC6472191
NM_014521SH3BP41
NM_006361HOXB131
NM_015541LRIG11
XM_943073LOC6478691
NM_030916PVRL41
NM_014751MTSS11
NM_003603SORBS21
NM_021069SORBS21
NM_0011016671
NM_003501ACOX31
NM_001013690LOC4017201
NM_015898ZBTB7A1
NM_032727INA1
NM_024653PRKRIP11
NM_015157PHLDB11
NM_032656DHX371
NM_007350PHLDA11
NM_025222TMEM1131
NM_003950F2RL31
NM_138347ZNF5511
NM_0010983981
NM_004371COPA1
NM_015282CLASP11
NM_0010988161
NM_006836GCN1L11
NM_148899FOXP21
NM_014491FOXP21
NM_148898FOXP21
NM_175733SYT91
NM_001543NDST11
NM_005368MB1
NM_203378MB1
NM_203377MB1
NM_0010853751
NM_002725PRELP1
NM_201348PRELP1
NM_178562TSPAN331
NM_021255PELI21
NM_025248SNIP1
NM_001006657WDR351
NM_020779WDR351
NM_174914UGT3A21
XM_378914KIAA04921
XM_944290KIAA04921
NM_001720BMP8B1
NM_181809BMP8A1
NM_001042486DLGAP41
NM_014902DLGAP41
NM_183006DLGAP41
NM_206909PSD31
NM_015310PSD31
NM_030815PDRG11
NM_007249KLF121
XM_371369MIA31
XM_943876MIA31
XM_943869MIA31
XM_943873MIA31
XM_496436MIA31
XM_932541MIA31
XM_932548MIA31
XM_001128037LOC7286541
XM_001129553LOC7314131
NM_006272S100B1
NM_001900CST51
NM_032353VPS251
NM_147193GLIS11
NM_012099CD3EAP1
NM_021130PPIA1
NM_014226RAGE1
NM_001007279RASL10A1
NM_001042724PVRL21
NM_178564NRBP21
NM_144618MGC298911
NM_144675GSG1L1
NM_0011097631
NM_001031746C10orf721
NM_001079843CASZ11
NM_152903KBTBD61
NM_024095ASB81
XM_001133059LOC7287721
XM_001133074LOC7287721
XM_001133066LOC7287721
NM_182746MCM41
NM_005914MCM41
NM_014898ZFP301
NM_145041TMEM106A1
NM_001632ALPP1
NM_145060C18orf241
NM_001039535C18orf241
NM_006716DBF41
NM_032374C14orf1531
NM_133375DIS3L1
NM_001033659FLJ358481
NM_012425RSU11
NM_152724RSU11
NM_152730C6orf1701
NM_006085BPNT11
NM_001018116LOC3472731
NM_022720DGCR81
NM_138425C12orf571
NM_015251ASCIZ1
NM_198066GNPNAT11
NM_198488FAM83H1
NM_058180C21orf581
NM_006060IKZF11
NM_001001713SH3BGR1
NM_007341SH3BGR1
NM_018049PLEKHJ11
NM_001040628NCALD1
NM_001040626NCALD1
NM_001040625NCALD1
NM_032041NCALD1
NM_001040629NCALD1
NM_001040624NCALD1
NM_001040627NCALD1
NM_001040630NCALD1
NM_032552DAB2IP1
XM_001130507LOC7317081
XM_001127823LOC7285731
NM_145265CCDC1271
NM_001964EGR11
XM_001124643LOC7304161

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