Automatic recommendation
OK - siRNA is specific for both sense and antisense (guide) strands
20 hits were found for GAGGCCUUGUGGUACUGCC (10 guide strand hits and 10 sense strand hits.)
Hits to Guide strand
Accession | Gene | Start | End | Details of mismatches | Spec. Score | Mismatches | Contiguous | Jackson style specificity | Hits similar gene | HSP Score | HSP % Identity | HSP length | Gene Length | ||||||||||||||||||
1 | 2 | 3 | 4 | 5 | 6 | 7 | 8 | 9 | 10 | 11 | 12 | 13 | 14 | 15 | 16 | 17 | 18 | 19 | |||||||||||||
NM_025155 | WDR71 | 468 | 486 | c | A | G | G | C | C | U | U | G | U | G | G | U | c | C | U | G | a | g | 70 | 4 | 12 | c | false | <90% | 1585 | ||
NM_001079871 | HAP1 | 2237 | 2255 | G | A | G | G | C | C | U | U | c | U | G | G | g | A | C | U | G | C | C | 29 | 2 | 8 | false | <90% | 3869 | |||
NM_001079870 | HAP1 | 2261 | 2279 | G | A | G | G | C | C | U | U | c | U | G | G | g | A | C | U | G | C | C | 29 | 2 | 8 | false | <90% | 3893 | |||
NM_177977 | HAP1 | 2312 | 2330 | G | A | G | G | C | C | U | U | c | U | G | G | g | A | C | U | G | C | C | 29 | 2 | 8 | false | <90% | 3944 | |||
NM_003949 | HAP1 | 2468 | 2486 | G | A | G | G | C | C | U | U | c | U | G | G | g | A | C | U | G | C | C | 29 | 2 | 8 | false | <90% | 4100 | |||
NM_172369 | C1QC | 1047 | 1065 | a | A | u | G | C | C | U | U | c | U | G | G | U | A | C | U | G | C | C | 18 | 3 | 10 | bc | false | <90% | 1171 | ||
NM_001017404 | LGR6 | 1873 | 1891 | G | A | G | G | C | C | g | U | G | U | G | G | g | A | C | U | G | C | g | 18 | 3 | 6 | false | <90% | 3041 | |||
NM_021636 | LGR6 | 2177 | 2195 | G | A | G | G | C | C | g | U | G | U | G | G | g | A | C | U | G | C | g | 18 | 3 | 6 | false | <90% | 3345 | |||
NM_001017403 | LGR6 | 2290 | 2308 | G | A | G | G | C | C | g | U | G | U | G | G | g | A | C | U | G | C | g | 18 | 3 | 6 | false | <90% | 3458 | |||
NM_013974 | DDAH2 | 1139 | 1157 | c | u | G | G | C | C | U | U | G | g | G | G | U | A | C | U | G | C | u | -1 | 4 | 8 | bc | false | <90% | 1351 |
Hits to Sense strand
Accession | Gene | Start | End | Details of mismatches | Spec. Score | Mismatches | Contiguous | Jackson style specificity | Hits similar gene | HSP Score | HSP % Identity | HSP length | Gene Length | ||||||||||||||||||
1 | 2 | 3 | 4 | 5 | 6 | 7 | 8 | 9 | 10 | 11 | 12 | 13 | 14 | 15 | 16 | 17 | 18 | 19 | |||||||||||||
XM_379904 | MUC12 | 1005 | 1023 | G | G | C | A | G | U | A | C | C | A | C | A | A | c | G | C | C | a | g | 72 | 3 | 13 | c | false | <90% | 5184 | ||
XM_379904 | MUC12 | 3079 | 3097 | G | G | C | A | G | U | A | C | C | A | C | A | A | c | G | C | C | a | g | 72 | 3 | 13 | c | false | <90% | 5184 | ||
NM_020170 | NCLN | 438 | 456 | a | G | C | A | G | U | A | C | C | A | g | A | A | G | G | C | C | c | u | 29 | 4 | 9 | c | false | <90% | 3749 | ||
NM_000283 | PDE6B | 807 | 825 | G | G | C | A | G | U | u | C | C | A | C | A | A | G | G | C | C | U | u | 28 | 2 | 11 | bc | false | <90% | 3283 | ||
NM_198889 | ANKRD17 | 323 | 341 | a | G | C | A | G | c | A | C | C | A | C | A | A | G | G | C | C | a | a | 27 | 4 | 11 | c | false | <90% | 8637 | ||
NM_032217 | ANKRD17 | 323 | 341 | a | G | C | A | G | c | A | C | C | A | C | A | A | G | G | C | C | a | a | 27 | 4 | 11 | c | false | <90% | 9390 | ||
NM_178468 | FAM83C | 1911 | 1929 | u | G | C | A | G | U | A | C | C | c | C | A | A | G | G | C | C | c | a | 7 | 4 | 8 | c | false | <90% | 3188 | ||
NM_004811 | LPXN | 457 | 475 | a | G | C | A | G | g | A | u | C | A | C | A | A | G | G | C | C | U | C | -27 | 3 | 11 | bc | false | <90% | 1875 | ||
NM_133499 | SYN1 | 1088 | 1106 | G | G | C | A | G | a | A | C | u | A | C | A | A | G | G | C | C | U | a | -28 | 3 | 9 | bc | false | <90% | 3172 | ||
NM_006950 | SYN1 | 1088 | 1106 | G | G | C | A | G | a | A | C | u | A | C | A | A | G | G | C | C | U | a | -28 | 3 | 9 | bc | false | <90% | 3210 |
3 prime UTR Seed matches
Hits to same gene : 0
Hits to other genes : 2596
View matched accessions
3 prime seed match details
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
Parameter | Spec. Score cut-off | Colour | Comment |
Hit to same gene | Colour | Hits 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 | ≥80 | Colour | Hits are very likely to cause an off-target effect |
Medium scoring hit | <80¸≥40 | Colour | Hits with a small chance of causing an off target effect. |
Low scoring hit | Colour | Hits very unlikely to cause an off-target effect |
The mismatches are colour coded based on the weighting of that position.
Cut-off | Colour |
Match | Colour |
Wobble base pairs (G-U) | Colour |
Critical bases (none) | Colour |
0.6 bits | Colour |
0.4 bits | Colour |
0.2 bits | Colour |
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