Automatic recommendation
OK - siRNA is specific for both sense and antisense (guide) strands
13 hits were found for GAAGGGAUGGUAUUGGAAA (10 guide strand hits and 3 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_001040659 | TTC23 | 2910 | 2928 | a | A | A | G | G | G | A | U | G | G | U | A | U | U | G | G | g | g | g | 66 | 4 | 15 | ac | false | <90% | 3245 | ||
| NM_001040658 | TTC23 | 3032 | 3050 | a | A | A | G | G | G | A | U | G | G | U | A | U | U | G | G | g | g | g | 66 | 4 | 15 | ac | false | <90% | 3367 | ||
| NM_001040657 | TTC23 | 3105 | 3123 | a | A | A | G | G | G | A | U | G | G | U | A | U | U | G | G | g | g | g | 66 | 4 | 15 | ac | false | <90% | 3440 | ||
| NM_001040656 | TTC23 | 3156 | 3174 | a | A | A | G | G | G | A | U | G | G | U | A | U | U | G | G | g | g | g | 66 | 4 | 15 | ac | false | <90% | 3491 | ||
| NM_022905 | TTC23 | 3227 | 3245 | a | A | A | G | G | G | A | U | G | G | U | A | U | U | G | G | g | g | g | 66 | 4 | 15 | ac | false | <90% | 3562 | ||
| NM_001040660 | TTC23 | 3351 | 3369 | a | A | A | G | G | G | A | U | G | G | U | A | U | U | G | G | g | g | g | 66 | 4 | 15 | ac | false | <90% | 3686 | ||
| NM_001040655 | TTC23 | 3473 | 3491 | a | A | A | G | G | G | A | U | G | G | U | A | U | U | G | G | g | g | g | 66 | 4 | 15 | ac | false | <90% | 3808 | ||
| NM_002147 | HOXB5 | 1457 | 1475 | a | A | A | G | G | G | A | U | G | G | U | A | U | U | G | a | g | A | A | 48 | 3 | 14 | c | false | <90% | 1830 | ||
| NM_005829 | AP3S2 | 397 | 415 | G | g | u | G | G | G | A | U | G | G | U | g | U | U | G | G | A | A | A | 35 | 3 | 8 | false | <90% | 2578 | |||
| NM_052880 | PIK3IP1 | 1360 | 1378 | c | A | A | G | G | G | A | U | G | G | c | A | U | U | G | a | A | A | A | 10 | 3 | 9 | c | false | <90% | 2443 | ||
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_017754 | C6orf107 | 5718 | 5736 | U | c | U | C | C | A | A | c | A | C | C | A | U | C | C | C | U | U | C | 26 | 2 | 11 | bc | false | <90% | 9658 | ||
| NM_181873 | MTMR11 | 2077 | 2095 | a | g | g | C | C | A | A | U | c | C | C | A | U | C | C | C | U | U | C | 6 | 4 | 10 | bc | false | <90% | 2324 | ||
| NM_016341 | PLCE1 | 2156 | 2174 | a | U | U | C | C | A | A | U | g | C | C | c | U | C | C | C | U | U | C | 4 | 3 | 7 | false | <90% | 7992 | |||
3 prime UTR Seed matches
Hits to same gene : 0
Hits to other genes : 3117
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