Automatic recommendation
OK - siRNA is specific for both sense and antisense (guide) strands
9 hits were found for GCUACUUCGUUGCUUCCUU (8 guide strand hits and 1 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_004960 | FUS | 43 | 61 | G | g | a | A | C | U | U | C | G | U | U | G | C | U | U | g | C | U | U | 42 | 3 | 12 | c | false | <90% | 2012 | ||
XM_942776 | SYNPO2 | 5680 | 5698 | u | C | U | A | C | U | U | C | a | U | U | G | C | U | U | u | C | U | U | 11 | 3 | 7 | c | false | <90% | 6839 | ||
XM_936336 | SYNPO2 | 5891 | 5909 | u | C | U | A | C | U | U | C | a | U | U | G | C | U | U | u | C | U | U | 11 | 3 | 7 | c | false | <90% | 7050 | ||
NM_133477 | SYNPO2 | 6122 | 6140 | u | C | U | A | C | U | U | C | a | U | U | G | C | U | U | u | C | U | U | 11 | 3 | 7 | c | false | <90% | 7318 | ||
NM_020354 | ENTPD7 | 2529 | 2547 | a | u | a | A | C | U | U | C | c | U | U | G | C | U | U | C | C | U | U | 6 | 4 | 10 | bc | false | <90% | 3040 | ||
NM_203394 | E2F7 | 4345 | 4363 | c | C | U | A | C | U | U | C | u | U | U | u | C | U | U | C | C | U | U | 4 | 3 | 7 | false | <90% | 5742 | |||
NM_005121 | THRAP1 | 5072 | 5090 | G | C | U | A | C | U | U | C | G | a | U | G | C | U | U | u | C | U | a | -13 | 3 | 9 | c | false | <90% | 10474 | ||
NM_020702 | KIAA1161 | 1497 | 1515 | G | C | U | A | C | U | c | C | G | U | g | G | C | U | U | C | C | U | U | -27 | 2 | 8 | c | false | <90% | 4185 |
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 | |||||||||||||
XR_018265 | LOC648124 | 2294 | 2312 | c | A | G | a | A | A | G | C | A | A | C | G | A | A | G | U | A | a | a | 53 | 4 | 13 | c | false | <90% | 2370 |
3 prime UTR Seed matches
Hits to same gene : 0
Hits to other genes : 2022
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