Predicted Off-targets for siRNA "ccgacuacuuugggugucc" 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 CCGACUACUUUGGGUGUCC (2 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_033238 PML 3122 3140 gCcACUACcUUGGGUGUCC18 3 10 bc false   <90%   5600
NM_000963 PTGS2 570 588 CCGACUcCcUUGGGUGUCa-31 3 9 bc false   <90%   4465



3 prime UTR Seed matches

Hits to same gene : 0
Hits to other genes : 137
View matched accessions

3 prime seed match details

AccessionGene nameHits to this gene
NM_197941ADAMTS61
NM_173510CCDC1171
NM_001561TNFRSF91
NM_003101SOAT11
NM_213605ZNF5171
NM_173670RGMB1
NM_178831GATS1
NM_001005611EDA1
XM_001134045LOC7299031
XM_001133484LOC7314981
NM_007174CIT1
NM_005239ETS21
NM_005437NCOA41
NM_020752GPR1581
NM_025195TRIB11
NM_024607PPP1R3B1
NM_014395DAPP11
NM_173547TRIM651
NM_002190IL17A1
NM_130785TPTE21
NM_199254TPTE21
NM_194317LYPD61
NM_032838ZNF5661
NM_182520C22orf151
NM_001364DLG21
NM_013351TBX211
NM_0011096891
NM_021061ZNF2501
XM_001128560LOC7311281
NM_002262KLRD11
NM_007334KLRD11
NM_001001414LOC3428971
NM_022549FEZ11
XM_001126700LOC7281471
XM_001126645LOC7306381
NM_001008493ENAH1
NM_018212ENAH1
NM_152288TMEM142C1
NM_001167BIRC41
NM_001776ENTPD11
NM_0010981751
NM_012420IFIT51
NM_014906PPM1E1
NM_206818OSCAR1
NM_021079NMT11
NM_001083621ZBTB401
NM_014870ZBTB401
NM_023037FRY1
NM_000217KCNA11
NM_016224SNX91
NM_001008408RBM331
NM_053043PRR81
NM_001001549GRB101
NM_001001555GRB101
NM_001001550GRB101
NM_005311GRB101
NM_145808MTPN1
XM_001133551LOC7317541
XM_001126119LOC7277571
NM_145899HMGA11
NM_145901HMGA11
NM_002131HMGA11
NM_145903HMGA11
NM_145902HMGA11
NM_145904HMGA11
NM_145905HMGA11
NM_198560LHFPL41
NM_023937MRPL341
NM_030576LIMD21
NM_203453PPAPDC21
NM_032242PLXNA11
NM_007175ERLIN21
NM_000068CACNA1A1
XM_498491LOC4399941
XM_930748LOC6423611
NM_017996DET11
NM_030788TM7SF41
XM_933796SLC45A41
NM_002829PTPN31
NM_014190ADD11
NM_176801ADD11
XM_001128169LOC7286871
NM_153456HS6ST31
NM_005001NDUFA71
NM_134433RFX21
NM_000635RFX21
NM_004992MECP21
NM_024866ADM21
NM_172037RDH101
NM_001918DBT1
NM_183373C6orf1451
XM_937537C6orf1451
NM_004728DDX211
NM_002827PTPN11
NM_001007139IGF21
NM_000612IGF21
NM_005228EGFR1
NM_001009812LBX21
NM_0207211
NM_153022C12orf591
NM_004200SYT71
XM_943686SYT71
NM_006367CAP11
NM_0011055301
NM_005222DLX61
NM_014663JMJD2A1
NM_016107ZFR1
NM_000243MEFV1
NM_006527SLBP1
NM_002251KCNS11
NM_003870IQGAP11
NM_021984GABRE1
NM_021987GABRE1
NM_004961GABRE1
NM_021990GABRE1
NM_003668MAPKAPK51
NM_139078MAPKAPK51
NM_005140CNGA21
NM_031309SCRT11
NM_000539RHO1
NM_006402HBXIP1
NM_007084SOX211
NM_001040667HSF41
NM_001538HSF41
NM_147168C9orf241
NM_032596C9orf241
NM_024665TBL1XR11
NM_0011031471
NM_0011031481
NM_0011031461
NM_015575TNRC151
NM_133367PAQR81
NM_000259MYO5A1
NM_181782NCOA71
NM_032797AIFM21
NM_0011127041
NM_052885SLC2A131

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