Automatic recommendation
OK - siRNA is specific for both sense and antisense (guide) strands
13 hits were found for GCACUUUAGUGACCUGGAA (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_014588 | VSX1 | 1836 | 1854 | G | C | A | C | U | U | U | A | G | U | G | A | C | u | U | G | G | A | u | 75 | 2 | 13 | c | false | <90% | 1956 | ||
| NM_024738 | C12orf49 | 2149 | 2167 | u | C | A | C | U | U | U | A | u | U | G | A | C | C | U | G | G | g | A | 35 | 3 | 8 | c | false | <90% | 2798 | ||
| NM_207325 | DPY19L3 | 2828 | 2846 | G | C | A | C | U | U | U | A | G | U | G | u | C | C | U | G | u | u | u | 35 | 4 | 11 | false | <90% | 4456 | |||
| NM_153018 | ZFP3 | 4481 | 4499 | G | C | A | a | U | U | U | A | G | U | G | A | C | C | U | G | u | u | g | 32 | 4 | 12 | c | false | <90% | 5011 | ||
| NM_001503 | GPLD1 | 2277 | 2295 | G | C | A | C | U | U | g | A | G | U | G | A | C | C | U | G | G | A | u | 28 | 2 | 11 | bc | false | <90% | 3489 | ||
| NM_020760 | HECW2 | 4891 | 4909 | G | g | A | C | U | U | g | A | G | U | G | A | C | C | U | G | G | A | A | 22 | 2 | 12 | bc | false | <90% | 6926 | ||
| NM_080591 | PTGS1 | 4233 | 4251 | G | C | A | C | U | U | U | A | a | U | G | g | C | C | U | G | G | A | g | 1 | 3 | 8 | false | <90% | 4982 | |||
| NM_000962 | PTGS1 | 4344 | 4362 | G | C | A | C | U | U | U | A | a | U | G | g | C | C | U | G | G | A | g | 1 | 3 | 8 | false | <90% | 5093 | |||
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_001077261 | NCOR2 | 3033 | 3051 | a | U | C | C | A | G | G | U | C | A | C | c | A | A | A | G | U | c | C | 61 | 3 | 10 | false | <90% | 8550 | |||
| NM_153705 | KDELC2 | 2947 | 2965 | g | U | u | C | A | G | u | U | C | A | C | U | A | A | A | G | U | G | C | 12 | 3 | 12 | bc | false | <90% | 4264 | ||
| NM_025231 | ZSCAN16 | 179 | 197 | U | U | C | C | A | G | c | U | C | A | C | a | A | A | A | G | U | G | C | 0 | 2 | 7 | false | <90% | 1290 | |||
| NM_004521 | KIF5B | 2835 | 2853 | g | a | a | C | A | G | c | U | C | A | C | U | A | A | A | G | U | G | C | 0 | 4 | 12 | bc | false | <90% | 3688 | ||
| NM_173529 | C18orf54 | 2414 | 2432 | U | U | C | C | A | G | G | U | u | A | a | U | A | A | A | G | U | G | u | -26 | 3 | 8 | c | false | <90% | 5016 | ||
3 prime UTR Seed matches
Hits to same gene : 0
Hits to other genes : 4043
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