Predicted Off-targets for siRNA "guuccgugcuauugagaaa" 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

12 hits were found for GUUCCGUGCUAUUGAGAAA (6 guide strand hits and 6 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_033048 CPXCR1 913 931 aUUCCGUGCUAUUGuGAgg65 4 13 c false   <90%   1609
NM_016413 CPB2 976 994 agUuCGUGCUAUUGAGAAA49 3 15 bc false   <90%   1603
NM_001872 CPB2 1087 1105 agUuCGUGCUAUUGAGAAA49 3 15 bc false   <90%   1766
NM_004999 MYO6 5593 5611 ugUCuGUGCUAUUGAGAAu30 4 13 bc false   <90%   8662
XM_938514 PRPF40A 3761 3779 uUUCCcUGCUAUUGAGgAA11 3 10 c false   <90%   7651
XM_371575 PRPF40A 4390 4408 uUUCCcUGCUAUUGAGgAA11 3 10 c false   <90%   8280


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_003112 SP4 2943 2961 UUUCUCuAUAGCACaGAAa4 3 7 c false   <90%   5811
NM_153277 SLC22A6 575 593 UUUCUCAAUgGCACaGAAg-12 3 9 c false   <90%   2025
NM_153278 SLC22A6 575 593 UUUCUCAAUgGCACaGAAg-12 3 9 c false   <90%   2064
NM_153279 SLC22A6 512 530 UUUCUCAAUgGCACaGAAg-12 3 9 c false   <90%   2131
NM_153276 SLC22A6 575 593 UUUCUCAAUgGCACaGAAg-12 3 9 c false   <90%   2194
NM_004790 SLC22A6 575 593 UUUCUCAAUgGCACaGAAg-12 3 9 c false   <90%   2196


3 prime UTR Seed matches

Hits to same gene : 0
Hits to other genes : 356
View matched accessions

3 prime seed match details

AccessionGene nameHits to this gene
NM_176081TRDMT12
NM_004412TRDMT12
NM_176083TRDMT12
NM_017660GATAD2A2
NM_002264KPNA12
NM_022459XPO41
NM_024817THSD41
NM_004232SOCS61
NM_007249KLF121
NM_001043SLC6A21
NM_032642WNT5B1
NM_030775WNT5B1
NM_138426GLCCI11
NM_019116UBFD11
NM_006606RBBP91
NM_000068CACNA1A1
NM_203327SLC23A21
NM_005116SLC23A21
NM_001025266LOC2853821
NM_173653SLC9A91
NM_014190ADD11
NM_176801ADD11
NM_033132ZIC51
NM_024949WWC21
NM_003118SPARC1
NM_020777SORCS21
NM_052995CLRN11
XM_001132728LOC7323141
XM_001128520LOC7287991
NM_001006620MAPKAP11
NM_001006619MAPKAP11
NM_001006621MAPKAP11
NM_024117MAPKAP11
NM_001006617MAPKAP11
NM_020245TULP41
NM_001007466TULP41
NM_178586PPP2R5C1
NM_002719PPP2R5C1
NM_001005473PLCXD31
NM_002096GTF2F11
NM_006862TDRKH1
NM_000831GRIK31
NM_016224SNX91
NM_005324H3F3B1
NM_139015SPPL31
NM_145893A2BP11
NM_145892A2BP11
NM_145891A2BP11
NM_004423DVL31
NM_053042KIAA17291
NM_016373WWOX1
NM_001077418FLJ221671
NM_001077416FLJ221671
NM_001077419FLJ221671
NM_001083913C10orf261
NM_017787C10orf261
NM_0011055731
NM_022080NAPB1
NM_016952CDON1
NM_153450MED191
NM_006358SLC25A171
NM_002784PSG91
NM_138736GNAO11
NM_213726INCA11
NM_001678ATP1B21
NM_004622TSN1
NM_014700RAB11FIP31
NM_006877GMPR1
NM_198149TMEM581
NM_175767IL6ST1
NM_183040DTNBP11
NM_014573TMEM971
NM_005881BCKDK1
NM_001039845MDH1B1
NM_022148CRLF21
NM_153675FOXA21
NM_021784FOXA21
NM_178520TMEM1051
NM_014931SAPS11
NM_001009998SSBP41
NM_032627SSBP41
NM_000391TPP11
NM_003004SECTM11
NM_138797ANKRD541
NM_001077426ZNF5861
XM_940362LOC6459841
XM_928946LOC6459841
NM_001080412ZBTB381
XM_001133510ZBTB381
NM_016548GOLPH21
NM_177937GOLPH21
NM_024630ZDHHC141
NM_153746ZDHHC141
NM_004438EPHA41
NM_012301MAGI21
NM_003734AOC31
NM_001015887IGSF111
NM_152538IGSF111
NM_001330CTF11
NM_003957BRSK21
NM_175056ZPLD11
NM_015995KLF131
NM_138412RDH131
NM_000512GALNS1
NM_004823KCNK61
NM_001201BMP31
NM_001440EXTL31
NM_005094SLC27A41
NM_001040446MTMR121
NM_006546IGF2BP11
NM_182503DEADC11
NM_004386NCAN1
NM_001032289SLC35A21
NM_001042498SLC35A21
NM_001407CELSR31
XM_001132233LOC7300531
XM_001134363FOXK21
XM_001134364FOXK21
NM_004514FOXK21
XM_943522LOC4410051
XM_498961LOC4410051
XM_001124624LOC7277281
NM_032449CC2D1B1
NM_194457UBE2J21
NM_194315UBE2J21
NM_058167UBE2J21
NM_194458UBE2J21
NM_001896CSNK2A21
NM_145020CCDC111
NM_001080415SR1401
XM_940802SR1401
NM_015102NPHP41
NM_007014WWP21
NM_199424WWP21
XM_001128001LOC7284011
XM_001127991LOC7284011
XM_001127568LOC7284991
XM_001127665LOC7285261
XM_001130826LOC7284521
XM_001127715LOC7285401
XM_001127825LOC7285751
XM_001130837LOC6433671
XM_932646LOC3400891
NM_138775ALKBH81
NM_031958KRTAP3-11
NM_019009TOLLIP1
NM_001688ATP5F11
NM_005766FARP11
NM_017656ZNF5621
NM_000376VDR1
NM_001017535VDR1
NM_001031680RUNX31
NM_004350RUNX31
NM_203286PVRL11
NM_016530RAB8B1
NM_001079878CNGA31
NM_001298CNGA31
NM_005806OLIG21
NM_178448C9orf1401
XM_001131234LOC7303381
XM_001126530LOC7305481
NM_013227ACAN1
NM_001135ACAN1
NM_001039517C1orf1041
NM_174917LOC1973221
NM_001007246BRWD11
NM_006454MXD41
NM_174936PCSK91
NM_173832ZFP411
NM_001025356TMEM16F1
NM_003215TEC1
NM_052845MMAB1
NM_024866ADM21
NM_212461PRKAG11
NM_002733PRKAG11
NM_001025100MBP1
NM_006643SDCCAG31
NM_001039708SDCCAG31
NM_001039707SDCCAG31
NM_005856RAMP31
NM_000634IL8RA1
XM_001132645ODZ31
XM_931600ODZ31
NM_001080477ODZ31
XM_940722ODZ31
NM_024785FAM124B1
NM_015140TTLL121
NM_199051FAM5C1
NM_005596NFIB1
NM_017799C14orf1011
NM_194272RBPMS21
NM_005312RAPGEF11
NM_198679RAPGEF11
NM_018649H2AFY21
NM_014811KIAA06491
XM_001132090LOC7300151
NM_214710PRSSL11
NM_182767SLC6A151
NM_032283ZDHHC181
NM_020697KCNS21
NM_003382VIPR21
NM_000033ABCD11
NM_138370LOC914611
NM_018045BSDC11
NM_014181HSPC1591
NM_001040715LOC6533191
NM_001040445ASB11
NM_004976KCNC11
NM_080668CDCA51
NM_013940OR10H11
NM_003724JRK1
NM_005523HOXA111
NM_001025780FAM108B11
NM_018697LANCL21
NM_014793LCMT21
NM_000727CACNG11
NM_145333MAP3K71
NM_145331MAP3K71
NM_145332MAP3K71
NM_003188MAP3K71
NM_0010987981
NM_0010987971
NM_0010987961
NM_032883TOX21
NM_002246KCNK31
NM_020338ZMIZ11
NM_152527SLC16A141
NM_001001132ITSN11
NM_052926PNMA51
NM_0011031511
NM_0011031501
NM_002428MMP151
NM_001009877BRD91
NM_023924BRD91
NM_020655JPH31
NM_139025ADAMTS131
NM_139027ADAMTS131
NM_139026ADAMTS131
NM_005277GPM6A1
NM_201592GPM6A1
NM_201591GPM6A1
XM_943661LRRC381
XM_059074LRRC381
NM_0011023671
NM_024952C14orf1591
NM_0011023661
NM_0011023691
NM_0011023681
NM_015604WDR21A1
NM_181340WDR21A1
NM_181341WDR21A1
NM_181552CUTL11
XM_944097LOC3896411
XM_374260LOC3896411
NM_0146871
NM_015833ADARB11
NM_015834ADARB11
NM_001112ADARB11
NM_001033049ADARB11
NM_005639SYT11
NM_004852ONECUT21
NM_004434EML11
NM_001008707EML11
XM_001125827LOC7278201
NM_030579CYB5B1
NM_152913TMEM1301
NM_0011013401
NM_173829P18SRP1
NM_022743SMYD31
NM_012064MIP1
NM_001964EGR11
NM_138782FCHO21
NM_003107SOX41
NM_017612ZCCHC81
NM_015947ASCC11
NM_003044SLC6A121
NM_005109OXSR11
NM_003071HLTF1
NM_133334WHSC11
NM_015265SATB21
XM_946142SHANK31
NM_001080420SHANK31
NM_002045GAP431
NM_0010976381
NM_000511FUT21
NM_016823CRK1
NM_005206CRK1
XM_001129896LOC7315081
NM_001078651TMEM1341
NM_025124TMEM1341
NM_001078650TMEM1341
NM_022377ICAM41
NM_020746VISA1
NM_020773TBC1D141
NM_024085ATG9A1
NM_001077198ATG9A1
NM_032843FIBCD11
NM_003792EDF11
NM_170744UNC5B1
NM_016358IRX41
NM_022893BCL11A1
NM_015892GALNAC4S-6ST1
NM_138717PPT21
NM_005155PPT21
NM_013279C11orf91
NM_024757EHMT11
NM_181716PRR61
XM_379636C9orf1221
XM_940165C9orf1221
NM_002523NPTX21
NM_0010987211
NM_0010987221
NM_004485GNG41
NM_031445AMMECR1L1
NM_022493NARFL1
NM_022003FXYD61
NM_173167UNC45B1
NM_001033576UNC45B1
NM_014956CEP1641
NM_001419ELAVL11
NM_152281SCYL1BP11
NM_006301MAP3K121
NM_001011513PDLIM51
NM_006457PDLIM51
NM_001033087C20orf1331
NM_080676C20orf1331
NM_001042371LOC2838711
NM_000833GRIN2A1
NM_198461LONRF21
NM_138959VANGL11
NM_138348FAM105B1
NM_001004333MGC719931
NM_005997VPS721
NM_031409CCR61
NM_004367CCR61
XM_039733KIAA09531
XM_940464KIAA09531
NM_001012427FOXP41
NM_138457FOXP41
NM_001012426FOXP41
NM_144566ZNF7001
NM_152443RDH121
NM_183397PXMP41
NM_007238PXMP41
NM_018449UBAP21
NM_021231C19orf291
NM_001080543C19orf291
NM_018715RCC21
NM_006948STCH1
NM_000368TSC11
NM_152493FLJ254761
NM_182832PLAC41
NM_004857AKAP51
NM_025251KIAA16881
NM_001083614EARS21
NM_016282AK31

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