Predicted Off-targets for siRNA "caacgagauggguuggcua" 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

5 hits were found for CAACGAGAUGGGUUGGCUA (0 guide strand hits and 5 sense strand hits.)

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_133378 TTN 79508 79526 aAGuCAACCCAUCaCGUUG41 3 9 c false   <90%   101519
NM_133437 TTN 60593 60611 aAGuCAACCCAUCaCGUUG41 3 9 c false   <90%   82604
NM_133432 TTN 60392 60410 aAGuCAACCCAUCaCGUUG41 3 9 c false   <90%   82403
NM_003319 TTN 60017 60035 aAGuCAACCCAUCaCGUUG41 3 9 c false   <90%   82028
NM_016620 ZNF644 40 58 UcaCCAACCCcUCUCGUUG7 3 8 c false   <90%   2085


3 prime UTR Seed matches

Hits to same gene : 0
Hits to other genes : 215
View matched accessions

3 prime seed match details

AccessionGene nameHits to this gene
NM_153266TMEM1512
XM_001133285TMEM1512
NM_015288PHF152
NM_019854PRMT81
NM_005828WDR681
XM_001129349LOC7283461
NM_001037165FOXK11
NM_000346SOX91
NM_032214SLA21
NM_175077SLA21
XM_001126310LOC7305511
XM_001130092LOC7293771
NM_024639ZNF322A1
NM_199005ZNF322B1
NM_000185SERPIND11
NM_080621SAMD101
NM_001012267CENPP1
NM_016276SGK21
NM_170693SGK21
NM_182503DEADC11
NM_023926ZSCAN181
NM_001080421UNC13A1
NM_139057ADAMTS171
NM_004852ONECUT21
NM_003010MAP2K41
NM_172239REXO1L11
XM_942952FLJ462841
XM_499123FLJ462841
NM_153620HOXA11
NM_014233UBTF1
NM_001076683UBTF1
NM_001076684UBTF1
NM_002509NKX2-21
NM_015055SWAP701
NM_021181SLAMF71
NM_025230WDR231
NM_181357WDR231
NM_001639APCS1
NM_0011107811
NM_003576STK241
NM_001032296STK241
NM_015264C22orf91
NM_001009880C22orf91
NM_153836CREG21
NM_024662NAT101
NM_017628KIAA15461
NM_005933MLL1
NM_017585SLC2A61
NM_032569N-PAC1
NM_003624RANBP31
NM_005431XRCC21
NM_001512GSTA41
NM_015659RSL1D11
NM_016169SUFU1
NM_002711PPP1R3A1
XM_942240LOC6505571
NM_182573LYPD51
NM_001031749LYPD51
NM_001918DBT1
NM_002577PAK21
NM_032208ANTXR11
NM_006312NCOR21
NM_001077261NCOR21
NM_030806C1orf211
NM_020933ZNF3171
NM_016520C9orf781
NM_000541SAG1
NM_138357CCDC109A1
NM_001001331ATP2B21
NM_001683ATP2B21
NM_006167NKX3-11
NM_017640LRRC161
NM_153015TMEM741
NM_005198CHKB1
NM_152253CHKB1
NM_177403RAB7B1
NM_007249KLF121
XM_001127016LOC7282621
NM_133638ADAMTS191
NM_152371C1orf931
NM_012072CD931
NM_004451ESRRA1
NM_0011003981
NM_015085GARNL41
NM_015995KLF131
NM_004992MECP21
XM_926336LOC6424511
XM_942222LOC6424511
NM_000324RHAG1
NM_006359SLC9A61
NM_001042537SLC9A61
NM_130459TOR2A1
NM_012279ZNF3461
NM_003107SOX41
NM_000228LAMB31
NM_001017402LAMB31
XM_928585LOC6532691
XM_929706LOC6537811
NM_0010997711
NM_005461MAFB1
NM_001802CDR21
NM_016433GLTP1
NM_017481UBQLN31
NM_032966BLR11
NM_001716BLR11
NM_015457ZDHHC51
XM_001130919LOC7296521
NM_018557LRP1B1
NM_001040659TTC231
NM_001040656TTC231
NM_001040658TTC231
NM_022905TTC231
NM_001040657TTC231
NM_001040655TTC231
NM_001040660TTC231
XM_001128616LOC4010211
NM_0251851
XM_929030LOC1615271
NM_001012446C9orf1281
NM_021905GABBR11
XM_934619LOC2845771
XM_945015LOC2845771
NM_001039904FLJ448381
NM_020836KIAA14461
NM_016078FAM18B1
XM_211174LOC2837101
XM_943482LOC2837101
NM_048368CTDP11
NM_001778CD481
NM_199454PRDM161
NM_022114PRDM161
NM_006048UBE4B1
NM_0011055621
NM_130469JDP21
NM_032342C9orf1251
NM_017433MYO3A1
NM_014770CENTG11
NM_015393DKFZP564O08231
NM_177539TAS1R11
XM_001132083LOC7321751
XM_001131915LOC7299671
NM_012280FTSJ11
NM_177439FTSJ11
NM_177434FTSJ11
NM_004947DOCK31
NM_002025AFF21
NM_001040633PRKAG21
NM_016203PRKAG21
NM_024429PRKAG21
NM_198458ZNF4971
NM_017776ZNF6731
NM_007108TCEB21
NM_004035ACOX11
NM_007292ACOX11
NM_016255FAM8A11
NM_017542POGK1
NM_024873TNIP31
NM_018383WDR331
NM_001551IGBP11
NM_000875IGF1R1
NM_014637MTFR11
NM_015156RCOR11
NM_022336EDAR1
NM_003918GYG21
NM_001079855GYG21
NM_177401MIDN1
NM_003602FKBP61
NM_014728FRMPD41
NM_022748TNS31
NM_178493NOTUM1
NM_017870TMEM132A1
NM_178031TMEM132A1
NM_178520TMEM1051
NM_001012993C9orf1521
XM_001125875LOC7278181
NM_015847MBD11
NM_015845MBD11
NM_015844MBD11
NM_002384MBD11
NM_015846MBD11
NM_016348C5orf41
NM_032385C5orf41
NM_019117KLHL41
NM_018170P15RS1
NM_002188IL131
NM_006122MAN2A21
NM_001077490GNAS1
NM_016592GNAS1
NM_199168CXCL121
NM_012328DNAJB91
NM_139199BRD81
NM_013411AK21
NM_033267IRX21
XM_934118LOC6534891
XM_934115LOC6534891
NM_004732KCNAB31
XM_495918FLJ132241
XM_938169FLJ132241
NM_001024457RGPD11
NM_015450POT11
NM_001042594POT11
NM_001226CASP61
NM_032992CASP61
NM_005497GJA71
NM_001080383GJA71
NM_001001665FLJ160081
XM_001124623LOC7277311
NM_005598NHLH11
NM_006190ORC2L1
NM_0229061
NM_015477SIN3A1
NM_152547BTNL91
NM_206966MGC239851
NM_0121941
NM_012081ELL21

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