Automatic recommendation
OK - siRNA is specific for both sense and antisense (guide) strands
8 hits were found for CCGACAAACACACCAAUUU (4 guide strand hits and 4 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_021575 | AP2S1 | 308 | 326 | a | C | G | c | C | A | A | A | C | A | C | A | C | C | A | A | c | U | U | 37 | 3 | 12 | c | false | <90% | 776 | ||
| NM_004069 | AP2S1 | 308 | 326 | a | C | G | c | C | A | A | A | C | A | C | A | C | C | A | A | c | U | U | 37 | 3 | 12 | c | false | <90% | 890 | ||
| NM_016059 | PPIL1 | 589 | 607 | a | C | G | g | C | A | A | A | C | A | C | A | C | C | A | u | U | U | U | 35 | 3 | 11 | c | false | <90% | 1723 | ||
| NM_005646 | TARBP1 | 4412 | 4430 | u | C | G | A | C | A | A | A | C | c | g | A | C | C | A | A | U | U | U | -46 | 3 | 8 | c | false | <90% | 5130 | ||
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_006187 | OAS3 | 6250 | 6268 | A | A | A | U | U | G | G | U | G | U | G | U | g | U | G | U | g | u | G | 63 | 3 | 12 | false | <90% | 6646 | |||
| NM_024939 | RBM35B | 2327 | 2345 | g | A | A | U | g | G | G | U | G | U | G | U | U | U | G | U | a | G | G | 23 | 3 | 11 | c | false | <90% | 4021 | ||
| XR_019031 | LOC649115 | 2764 | 2782 | g | A | A | U | U | G | u | U | G | U | G | U | U | U | G | U | u | G | G | 8 | 3 | 9 | c | false | <90% | 3004 | ||
| NM_030579 | CYB5B | 2699 | 2717 | A | A | A | U | U | G | G | U | G | U | u | U | U | U | G | U | u | a | u | 7 | 4 | 10 | c | false | <90% | 4286 | ||
3 prime UTR Seed matches
Hits to same gene : 0
Hits to other genes : 209
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)
Motif found in sense strand
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