Automatic recommendation
Not OK - siRNA is not specific
10 hits were found for UUAGGUAGAGUAAUAUACG (5 guide strand hits and 5 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_152774 | MGC42090 | 3780 | 3798 | a | U | A | G | G | U | A | G | A | G | U | A | u | U | A | U | A | a | G | 84 | 3 | 11 | false | <90% | 3992 | |||
| NM_001010986 | ATP11C | 3682 | 3700 | U | U | A | G | u | U | A | G | A | G | U | A | A | U | A | U | A | a | c | 40 | 3 | 12 | c | false | <90% | 6030 | ||
| NM_173694 | ATP11C | 3787 | 3805 | U | U | A | G | u | U | A | G | A | G | U | A | A | U | A | U | A | a | c | 40 | 3 | 12 | c | false | <90% | 6135 | ||
| NM_019021 | C11orf71 | 1404 | 1422 | U | U | A | G | G | U | A | c | A | G | U | A | A | U | A | a | A | C | a | 6 | 3 | 7 | c | false | <90% | 1466 | ||
| NM_006418 | OLFM4 | 1968 | 1986 | U | U | A | G | G | U | A | G | A | u | U | A | A | U | A | U | c | u | G | -8 | 3 | 9 | c | false | <90% | 2844 | ||
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_019539 | LOC652445 | 332 | 350 | a | G | U | A | U | A | U | U | A | C | U | C | U | A | C | a | U | u | g | 64 | 4 | 14 | c | false | <90% | 1468 | ||
| XR_016034 | LOC729960 | 332 | 350 | a | G | U | A | U | A | U | U | A | C | U | C | U | A | C | a | U | u | g | 64 | 4 | 14 | c | false | <90% | 1468 | ||
| NM_016931 | NOX4 | 1249 | 1267 | a | G | U | A | U | A | U | U | A | C | U | C | U | A | C | a | U | u | g | 64 | 4 | 14 | c | false | <90% | 2416 | ||
| NM_020159 | SMARCAD1 | 3881 | 3899 | u | G | c | A | U | A | U | U | A | C | U | C | U | g | C | C | U | A | A | 58 | 3 | 10 | c | false | <90% | 4934 | ||
| NM_207337 | AMN1 | 686 | 704 | C | G | U | A | U | A | U | U | A | C | U | C | U | u | C | C | a | u | g | 49 | 4 | 13 | c | false | <90% | 1979 | ||
3 prime UTR Seed matches
Hits to same gene : 0
Hits to other genes : 1289
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