Automatic recommendation
Not OK - siRNA is not specific
13 hits were found for CCAACUGUAACUUAGAAGU (8 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_201647 | STAMBP | 1539 | 1557 | g | C | A | A | C | U | G | U | A | A | C | U | c | A | G | A | A | a | U | 84 | 3 | 11 | false | <90% | 1967 | |||
| NM_006463 | STAMBP | 1678 | 1696 | g | C | A | A | C | U | G | U | A | A | C | U | c | A | G | A | A | a | U | 84 | 3 | 11 | false | <90% | 2106 | |||
| NM_213622 | STAMBP | 1992 | 2010 | g | C | A | A | C | U | G | U | A | A | C | U | c | A | G | A | A | a | U | 84 | 3 | 11 | false | <90% | 2417 | |||
| XM_926336 | LOC642451 | 17 | 35 | g | a | A | A | C | U | G | U | A | A | C | U | U | A | c | A | A | G | a | 56 | 4 | 12 | c | false | <90% | 1805 | ||
| XM_942222 | LOC642451 | 17 | 35 | g | a | A | A | C | U | G | U | A | A | C | U | U | A | c | A | A | G | a | 56 | 4 | 12 | c | false | <90% | 1805 | ||
| NM_015938 | NMD3 | 1261 | 1279 | C | C | A | A | C | U | G | U | A | A | C | U | U | A | a | A | u | G | a | 46 | 3 | 14 | c | false | <90% | 2758 | ||
| XR_015991 | LOC729374 | 546 | 564 | u | C | A | A | a | U | G | U | A | A | C | U | U | A | G | A | A | a | a | 38 | 4 | 12 | c | false | <90% | 1107 | ||
| NM_174916 | UBR1 | 6189 | 6207 | a | C | A | A | C | U | G | U | A | A | a | U | U | A | G | A | A | c | a | 29 | 4 | 9 | c | false | <90% | 7758 | ||
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 | |||||||||||||
| NM_007203 | PALM2-AKAP2 | 3356 | 3374 | A | C | U | U | C | U | A | A | G | U | U | A | C | u | G | U | c | u | u | 49 | 4 | 13 | c | false | <90% | 7522 | ||
| NM_001042604 | XRN1 | 3412 | 3430 | A | C | U | U | C | U | c | A | G | U | U | c | C | A | G | U | U | G | G | 0 | 2 | 7 | false | <90% | 10053 | |||
| NM_019001 | XRN1 | 3412 | 3430 | A | C | U | U | C | U | c | A | G | U | U | c | C | A | G | U | U | G | G | 0 | 2 | 7 | false | <90% | 10092 | |||
| XM_375697 | OTUD3 | 3613 | 3631 | g | C | U | U | u | U | c | A | G | U | U | A | C | A | G | U | U | G | G | -19 | 3 | 12 | bc | false | <90% | 6621 | ||
| XM_939048 | OTUD3 | 3613 | 3631 | g | C | U | U | u | U | c | A | G | U | U | A | C | A | G | U | U | G | G | -19 | 3 | 12 | bc | false | <90% | 6621 | ||
3 prime UTR Seed matches
Hits to same gene : 0
Hits to other genes : 1686
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