Predicted Off-targets for siRNA "gcaacggcacuaaacacaa" 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

4 hits were found for GCAACGGCACUAAACACAA (1 guide strand hits and 3 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_175907 ZADH2 2854 2872 aCAACuGCACUAAAgACAA9 3 8 c false   <90%   4132


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_001497 B4GALT1 803 821 UUGUGUUUAGUGaCGUgGa61 3 12   false   <90%   4080
NM_181791 GPR141 891 909 UUGUGUUUuGUGCCGUUag32 3 8 c false   <90%   918
NM_022744 C16orf58 2349 2367 UUGUGUUUAaaGCCGUUGg-49 3 9 c false   <90%   2760


3 prime UTR Seed matches

Hits to same gene : 0
Hits to other genes : 240
View matched accessions

3 prime seed match details

AccessionGene nameHits to this gene
NM_031445AMMECR1L2
XM_940069PPP1R3E2
XM_927029PPP1R3E2
NM_020825CRAMP1L2
NM_032561C22orf232
NM_014363SACS1
NM_024947PHC31
NM_018082POLR3B1
XM_929714LOC6467621
XM_935722LOC6467621
XM_938418LOC6467621
NM_014613UBXD81
NM_1449931
NM_003439ZKSCAN11
NM_000849GSTM31
NM_020770CGN1
XM_944835LOC6486911
NM_003102SOD31
NM_006048UBE4B1
NM_0011055621
NM_018983NOLA11
NM_032993NOLA11
NM_015187KIAA07461
NM_175862CD861
NM_006889CD861
NM_002395ME11
XM_945643LOC2564831
XM_173015LOC2564831
NM_001040152PEG101
NM_015068PEG101
NM_153481IL17RE1
NM_153483IL17RE1
NM_153480IL17RE1
NM_001077620PRCD1
NM_020184CNNM41
NM_080833C20orf1511
XM_001131466LOC7285161
XM_001132985LOC7311771
NM_012398PIP5K1C1
NM_023016ANKRD571
NM_024768CCDC481
XM_934619LOC2845771
XM_945015LOC2845771
NM_175066DDX511
NM_014470RND11
NM_078483SLC36A11
NM_030774OR51E21
NM_153340ATXN7L21
NM_004822NTN11
NM_178554KY1
NM_015545PTCD11
NM_001080543C19orf291
NM_024311MFSD111
NM_018373SYNJ2BP1
NM_007163SLC14A21
NM_003036SKI1
NM_012083FRAT21
NM_145004ADAM321
NM_012315KLK91
NM_001037325CCDC461
NM_145036CCDC461
NM_004100EYA41
NM_172105EYA41
NM_172103EYA41
NM_153270KLHL341
XM_940609FLJ250761
XM_059689FLJ250761
NM_014590ERVWE11
NM_021197WFDC11
NM_001014283DCUN1D21
NM_005239ETS21
NM_020806GPHN1
NM_001024218GPHN1
NM_006017PROM11
NM_001045478LOC6449971
NM_197949CLEC7A1
NM_197950CLEC7A1
NM_022570CLEC7A1
NM_197948CLEC7A1
NM_197947CLEC7A1
NM_0010992721
NM_152733BTBD91
NM_0528931
NM_023947CHID11
XM_001131408LOC7303501
XM_001127666LOC7308961
NM_001008709PPP1CA1
NM_206873PPP1CA1
NM_002708PPP1CA1
NM_032012C9orf51
NM_0010997341
NM_012409PRND1
NM_015347RIMBP21
NM_018970GPR851
NM_001030287ATF31
NM_001674ATF31
NM_004024ATF31
NM_001040619ATF31
NM_0024581
NM_031950FGFBP21
NM_013994DDR11
NM_013993DDR11
NM_001954DDR11
NM_024017HOXB91
NM_000438PAX31
NM_013942PAX31
NM_001043318C14orf431
NM_194278C14orf431
NM_015253WSCD11
NM_006026H1FX1
NM_032560SMEK11
NM_021012KCNJ121
NM_016952CDON1
XM_001133286CDON1
NM_182935MOBP1
NM_175861TMTC11
NM_002760PRKY1
NM_001039884FLJ448941
NM_031310PLVAP1
NM_020796SEMA6A1
NM_001081976ADORA31
NM_020683ADORA31
NM_022459XPO41
NM_031208FAHD11
NM_032028TSSK1B1
NM_014586HUNK1
NM_004200SYT71
XM_943686SYT71
NM_001001389CD441
NM_001001390CD441
NM_001001391CD441
NM_001001392CD441
NM_000610CD441
NM_018234STEAP31
NM_001008410STEAP31
NM_182915STEAP31
NM_014867KBTBD111
NM_001080484KIAA17511
XM_936307KIAA17511
NM_006516SLC2A11
NM_032423ZNF5281
NM_001754RUNX11
NM_001001890RUNX11
NM_001079539XBP11
NM_005080XBP11
NM_033225CSMD11
NM_001077196PDE11A1
NM_001077197PDE11A1
NM_016953PDE11A1
NM_024933ANKRD531
NM_017945SLC35A51
NM_145064STAC31
NM_021143ZNF201
NM_001013640LOC3885031
NM_001017995SH3PXD2B1
NM_000960PTGIR1
NM_0011008291
NM_207405FLJ464811
NM_0010854291
NM_004104FASN1
NM_182527CABP71
NM_007274ACOT71
NM_181865ACOT71
NM_181866ACOT71
NM_181864ACOT71
NM_003969UBE2M1
NM_001002814RAB11FIP11
NM_014615KIAA01821
NM_144586LYPD11
NM_001077427LYPD11
NM_033260FOXQ11
NM_006382CDRT11
NM_031444C22orf131
NM_006464TGOLN21
NM_031845MAP21
NM_031847MAP21
NM_001039538MAP21
NM_002374MAP21
NM_024795TM4SF201
NM_002507NGFR1
NM_005683GPR551
NM_031918KLF161
NM_015111N4BP31
NM_0152761
NM_007223GPR1761
NM_003695LY6D1
NM_006393NEBL1
NM_017712PGPEP11
NM_004788UBE4A1
NM_032642WNT5B1
NM_030775WNT5B1
NM_015033FNBP11
XM_942964LOC2864111
XM_932619LOC2864111
NM_032207C19orf441
NM_002657PLAGL21
NM_147187TNFRSF10B1
NM_003842TNFRSF10B1
XM_001133820LOC7297761
NM_001042599ERBB41
NM_005235ERBB41
XM_925864LOC6423251
XM_929030LOC1615271
XM_933066LOC6436961
NM_001001694FLJ419931
NM_014155ZBTB441
NM_022965FGFR31
NM_000142FGFR31
NM_021932RIC8A1
NM_004125LOC5528911
NM_001017998GNG101
NM_001008539SLC7A21
NM_003046SLC7A21
NM_020422TMEM1591
XM_943034LOC6430851
XM_931304LOC6430851
NM_133448TMEM132D1
NM_014798PLEKHM11
XM_001128220PLEKHM11
NM_0010988111
NM_007345ZNF2361
NM_006165NFRKB1
NM_178569C5orf381
NM_006363SEC23B1
NM_032986SEC23B1
NM_032985SEC23B1
XM_927238LOC6439881
XM_936418LOC6473471
NM_002622PFDN11
NM_001024843TNRC6B1
NM_015088TNRC6B1
NM_000705ATP4B1
NM_000167GK1
NM_203391GK1
NM_144775SMCR81
NM_001080498EMR41
NM_016258YTHDF21
NM_007220CA5B1
NM_017658KLHL281
NM_0177821

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)
Motif found in sense strand

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