Predicted Off-targets for siRNA "cgcaccggggauccuaggc" 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

7 hits were found for CGCACCGGGGAUCCUAGGC (2 guide strand hits and 5 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_001877 CR2 136 154 CGCACCGGGGgUCCUcGGg7 3 10 c false   <90%   3982
NM_001006658 CR2 136 154 CGCACCGGGGgUCCUcGGg7 3 10 c false   <90%   4159


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_001077621 VPS37D 870 888 cggUAGGAUCCaCGGUGCG33 4 8   false   <90%   1609
XM_943032 LOC647805 685 703 GCCUAGcAUCCaCGGUGCG0 2 7   false   <90%   1182
NM_021872 CDC25B 896 914 uCCUgGGgUCCCCGGUGCG-15 3 11 bc false   <90%   3578
NM_004358 CDC25B 896 914 uCCUgGGgUCCCCGGUGCG-15 3 11 bc false   <90%   3659
NM_021873 CDC25B 896 914 uCCUgGGgUCCCCGGUGCG-15 3 11 bc false   <90%   3701


3 prime UTR Seed matches

Hits to same gene : 0
Hits to other genes : 168
View matched accessions

3 prime seed match details

AccessionGene nameHits to this gene
NM_014844KIAA03293
NM_001031617COX192
NM_001040661SLC29A42
NM_153247SLC29A42
NM_001560IL13RA11
NM_139159DPP91
NM_001042574CRTC31
NM_022769CRTC31
NM_004114FGF131
NM_033642FGF131
NM_001044370MPPED11
NM_002375MAP41
NM_030884MAP41
XM_495918FLJ132241
XM_938169FLJ132241
XM_931281LOC6430721
XM_943769LOC6430721
NM_207348SLC25A341
NM_001039577CCNL21
NM_004992MECP21
XM_001130238LOC7282831
XM_001132687LOC7310871
XM_938028C19orf161
NM_000080CHRNE1
XM_001132270LOC7300011
XM_001131474LOC7303411
XM_001131575LOC7318971
NM_178448C9orf1401
NM_207396RNF2071
NM_176871PDLIM21
NM_001082575HRNBP31
NM_013304ZDHHC11
NM_000278PAX21
NM_003989PAX21
NM_003990PAX21
NM_003987PAX21
NM_003988PAX21
NM_153256C10orf471
NM_002688SEPT51
NM_182551LYCAT1
NM_001002257LYCAT1
NM_005061RPL3L1
NM_152219GJC11
NM_173476CCDC781
XM_001128427LOC7287681
XM_940977LOC6517581
NM_024919FRMD11
NM_001037SCN1B1
NM_001008407BCAP291
NM_000832GRIN11
NM_007327GRIN11
NM_021569GRIN11
NM_005036PPARA1
NM_001001928PPARA1
NM_206833CTXN11
XM_936809LOC3429181
XM_292779LOC3429181
NM_001042573FLJ218651
NM_005806OLIG21
NM_024329EFHD21
NM_005170ASCL21
NM_001039966GPR301
NM_001505GPR301
NM_0010982011
NM_020134DPYSL51
NM_016155MMP171
XM_001133320MMP171
NM_001043318C14orf431
NM_194278C14orf431
NM_001045477FAM22G1
NM_001846COL4A21
NM_002105H2AFX1
XM_930750LOC6423661
XM_943652LOC6423661
NM_058192RPUSD11
NM_199461NANOS11
NM_001420ELAVL31
NM_032281ELAVL31
NM_002861PCYT21
NM_005226EDG31
NM_012140SLC25A101
NM_005883APC21
NM_198253TERT1
NM_198255TERT1
XM_495939KIAA15451
XM_936428KIAA15451
NM_006645STARD101
NM_006224PITPNA1
NM_024877CNTD21
NM_198850PHLDB31
XM_928224LOC6535831
XM_001131797LOC7320751
NM_002342LTBR1
NM_020230PPAN1
XM_931359LOC3387581
XM_944677LOC3387581
NM_053045MGC143271
XM_936119LOC6420441
XM_936165LOC6420751
XM_933843LOC6467201
XM_945002LOC6518951
NM_005479FRAT11
NM_0010853771
NM_002387MCC1
NM_015461ZNF5211
NM_014964EPN21
NM_0011026641
NM_148921EPN21
NM_032389ZNF2891
XM_001134463BAHCC11
NM_001080519BAHCC11
XM_936831IQSEC31
NM_014665LRRC141
NM_006943SOX121
NM_032737LMNB21
NM_001004439ITGA111
XM_932244LOC6531601
XM_945233LOC6531601
NM_001029885MGC103341
NM_182553CNIH21
XM_001129488CNIH21
NM_207333ZNF3201
NM_207419C1QTNF81
NM_0209081
NM_005078TLE31
NM_0011051921
NM_000151G6PC1
NM_004286GTPBP11
NM_001018070CORO1B1
NM_020441CORO1B1
NM_000748CHRNB21
XM_933935LOC6467781
XM_943239LOC6467781
NM_014661FAM53B1
NM_031215CABLES21
NM_002911UPF11
NM_000599IGFBP51
NM_013435RAX1
NM_018027FRMD4A1
NM_019884GSK3A1
NM_145685BRF11
NM_001519BRF11
NM_001049SSTR11
NM_178500PHOSPHO11
NM_152494DCST11
NM_021025TLX31
NM_017953C1orf1811
NM_178167ZNF5981
NM_130459TOR2A1
NM_181804PKIG1
NM_181805PKIG1
NM_007066PKIG1
NM_001495GFRA21
NM_032246RKHD31
NM_001024227ARF11
NM_001658ARF11
NM_001024228ARF11
NM_001024226ARF11
NM_020132AGPAT31
NM_001037553AGPAT31
NM_000629IFNAR11
NM_004535MYT11
NM_001042413GLIS31
NM_152629GLIS31
NM_003648DGKD1
NM_152879DGKD1
NM_001040701FUT61
NM_000150FUT61

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