Predicted Off-targets for siRNA "acgccuauccaugacgcaa" 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

1 hit was found for ACGCCUAUCCAUGACGCAA (1 guide strand hits and 0 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_003415 ZNF268 56 74 uuGCCUcUCCAUGACGCAA20 3 12 bc false   <90%   3826



3 prime UTR Seed matches

Hits to same gene : 0
Hits to other genes : 247
View matched accessions

3 prime seed match details

AccessionGene nameHits to this gene
NM_006122MAN2A22
NM_001289CLIC22
NM_022063C10orf841
NM_005971FXYD31
NM_021910FXYD31
NM_005895GOLGA31
NM_001042584CD1E1
NM_001042587CD1E1
NM_153631HOXA31
NM_153632HOXA31
NM_030661HOXA31
NM_003679KMO1
NM_030806C1orf211
NM_003747TNKS1
NM_024733ZNF6651
NM_0011055761
NM_002716PPP2R1B1
NM_018210FLJ107691
NM_014999RAB211
NM_173561UNC5CL1
NM_003449TRIM261
NM_201266NRP21
NM_003872NRP21
NM_201279NRP21
NM_003786ABCC31
NM_207405FLJ464811
NM_018322C6orf641
NM_025015HSPA12A1
NM_001386DPYSL21
NM_001080975REPS21
NM_004726REPS21
XM_001127950LOC7305661
XM_001133333LOC7291721
NM_017921NPLOC41
NM_152470RNF1651
NM_001012393OPCML1
NM_002545OPCML1
NM_005253FOSL21
NM_018429BDP11
NM_007174CIT1
NM_013365GGA11
NM_001001560GGA11
NM_201544LGALS81
NM_006499LGALS81
NM_201545LGALS81
NM_201543LGALS81
XM_498479LOC4399621
XM_001129151LOC7290471
XM_938194LOC1276021
XM_059166LOC1276021
NM_001083591CUGBP21
NM_001025077CUGBP21
NM_006561CUGBP21
NM_001025076CUGBP21
XM_037557KIAA09841
XM_939476KIAA09841
NM_001153ANXA41
NM_014788TRIM141
NM_133473ZNF4311
XM_376795FLJ458721
XM_940037FLJ458721
NM_005180BMI11
NM_139283PPTC71
NM_032515BOK1
NM_014631SH3PXD2A1
NM_030965ST6GALNAC51
NM_138967SCAMP51
NM_181283CMTM11
NM_181270CMTM11
NM_181268CMTM11
NM_181296CMTM11
XM_001133211LOC7290031
XM_001133556LOC7291351
NM_001031681CTNS1
NM_004937CTNS1
NM_002911UPF11
NM_014139SCN11A1
NM_024541C10orf761
NM_012183FOXD31
NM_032109OTP1
NM_005634SOX31
NM_013422ARHGAP61
NM_006125ARHGAP61
NM_212467CAPN31
NM_016173HEMK11
NM_012253TKTL11
NM_007184NISCH1
NM_020786PDP21
NM_0010853771
NM_002387MCC1
NM_005319HIST1H1C1
NM_002336LRP61
NM_144712SLC23A31
NM_006357UBE2E31
NM_182678UBE2E31
NM_000337SGCD1
NM_0155661
NM_017684VPS13C1
NM_020821VPS13C1
NM_032296FLYWCH11
NM_004571PKNOX11
NM_017521FEV1
NM_175571GIMAP81
NM_004936CDKN2B1
NM_078487CDKN2B1
NM_017848FAM120C1
NM_198999SLC26A51
NM_018200HMG20A1
NM_000442PECAM11
XM_001127604NFATC2IP1
NM_032815NFATC2IP1
NM_001007525NWD11
NM_033224PURB1
NM_024022TMPRSS31
NM_032404TMPRSS31
NM_032401TMPRSS31
NM_002688SEPT51
NM_145298APOBEC3F1
NM_018242FLJ108471
NM_019042PUS71
NM_207322NLF11
NM_0010895841
NM_001348DAPK31
NM_006133DAGLA1
NM_153456HS6ST31
NM_014573TMEM971
NM_001006630CHRM21
NM_001006632CHRM21
NM_001006626CHRM21
NM_001006629CHRM21
NM_001006627CHRM21
NM_001006631CHRM21
NM_000739CHRM21
NM_001006628CHRM21
NM_003045SLC7A11
NM_006389HYOU11
NM_014926SLITRK31
NM_012405ICMT1
NM_145733SEPT31
NM_019106SEPT31
NM_001080485ZNF2751
NM_032420PCDH11
NM_014299BRD41
NM_181337KAAG11
NM_206538LOC2843611
NM_175063LOC2843611
NM_001017523BTBD111
NM_001018072BTBD111
NM_001080421UNC13A1
NM_016248AKAP111
NM_015147CEP681
NM_001031617COX191
XM_001126962LOC7280321
NM_016946F11R1
NM_182922HEATR31
NM_152269C12orf651
XM_001134250LOC7320531
NM_173825RABL31
XM_926634LOC6532561
XM_001126849LOC7279001
NM_014285EXOSC21
NM_001001479SLC35E41
XM_001133026LOC7313861
XM_001133204LOC7291201
NM_0011006241
NM_033064ATCAY1
NM_004857AKAP51
NM_001001701LOC4011521
XM_941062FLJ418561
XM_371176FLJ418561
NM_032933C18orf451
NM_017861PIGX1
NM_005160ADRBK21
NM_024512LRRC21
NM_005793NME61
NM_015071ARHGAP261
NM_1523571
NM_001033055AIPL11
NM_001033054AIPL11
NM_014336AIPL11
NM_032374C14orf1531
NM_000877IL1R11
NM_004646NPHS11
NM_025104DBF4B1
XM_001133565LOC7314401
NM_001039796FLJ357761
NM_152916EMR21
NM_152918EMR21
NM_152917EMR21
NM_152920EMR21
NM_152921EMR21
NM_013447EMR21
NM_152919EMR21
NM_152263TPM31
XM_927706LOC6445911
NM_174977SEC14L41
NM_015044GGA21
NM_001099ACPP1
NM_014326DAPK21
NM_015040PIP5K31
NM_198460GBP61
NM_003950F2RL31
NM_023923PHACTR41
NM_001048183PHACTR41
NM_006864LILRB31
NM_001081450LILRB31
NM_004823KCNK61
NM_005076CNTN21
NM_004050BCL2L21
NM_006731FCMD1
NM_001079802FCMD1
NM_003757EIF3S21
NM_003167SULT2A11
NM_017929PEX261
NM_138468ICA1L1
NM_181521CMTM41
NM_024782NHEJ11
NM_006139CD281
NM_019064SDK21
NM_006359SLC9A61
NM_001042537SLC9A61
NM_004796NRXN31
NM_0011052501
NM_138970NRXN31
NM_144973MGC240391
NM_001066TNFRSF1B1
NM_005780LHFP1
NM_198213OASL1
NM_175744RHOC1
NM_001042679RHOC1
NM_001042678RHOC1
XM_939663KIAA15531
NM_001080450KIAA15531
NM_153825SLA/LP1
NM_000833GRIN2A1
XM_944564MGC158851
XM_378517MGC158851
NM_152464C17orf321
NM_025059C6orf971
NM_001082480ZNF6231
NM_014789ZNF6231
NM_002536TBC1D251
NM_001005463EBF31
NM_033128SCIN1
NM_0011127061
NM_014520MYBBP1A1
NM_175062RASGEF1C1

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