Automatic recommendation
OK - siRNA is specific for both sense and antisense (guide) strands
18 hits were found for GCUCAUAUUGUUAUUGAUA (12 guide strand hits and 6 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 | |||||||||||||
| XR_017165 | LOC400592 | 690 | 708 | G | C | U | C | A | U | A | U | U | G | U | a | u | U | U | G | A | U | u | 50 | 3 | 11 | false | <90% | 1408 | |||
| NM_001126 | ADSS | 691 | 709 | G | C | U | C | A | U | A | U | U | G | U | a | u | U | U | G | A | U | u | 50 | 3 | 11 | false | <90% | 2775 | |||
| NM_001726 | BRDT | 412 | 430 | u | C | U | C | A | a | A | U | U | G | U | U | A | U | U | u | A | U | A | 8 | 3 | 9 | c | false | <90% | 3119 | ||
| NM_207189 | BRDT | 450 | 468 | u | C | U | C | A | a | A | U | U | G | U | U | A | U | U | u | A | U | A | 8 | 3 | 9 | c | false | <90% | 3157 | ||
| XM_001127587 | FLJ32810 | 1306 | 1324 | c | C | U | g | A | U | A | U | U | G | a | U | A | U | U | G | A | U | A | 0 | 3 | 8 | c | false | <90% | 4820 | ||
| XM_001127623 | FLJ32810 | 1306 | 1324 | c | C | U | g | A | U | A | U | U | G | a | U | A | U | U | G | A | U | A | 0 | 3 | 8 | c | false | <90% | 4820 | ||
| XM_925815 | FLJ32810 | 1306 | 1324 | c | C | U | g | A | U | A | U | U | G | a | U | A | U | U | G | A | U | A | 0 | 3 | 8 | c | false | <90% | 4820 | ||
| XM_001127637 | FLJ32810 | 1309 | 1327 | c | C | U | g | A | U | A | U | U | G | a | U | A | U | U | G | A | U | A | 0 | 3 | 8 | c | false | <90% | 4823 | ||
| XM_001127597 | FLJ32810 | 1315 | 1333 | c | C | U | g | A | U | A | U | U | G | a | U | A | U | U | G | A | U | A | 0 | 3 | 8 | c | false | <90% | 4829 | ||
| NM_007249 | KLF12 | 1742 | 1760 | a | g | a | C | A | U | u | U | U | G | U | U | A | U | U | G | A | U | A | 0 | 4 | 12 | bc | false | <90% | 10923 | ||
| NM_173829 | P18SRP | 6702 | 6720 | G | C | U | u | A | U | c | U | U | G | U | U | A | U | U | G | A | U | A | -3 | 2 | 12 | bc | false | <90% | 6856 | ||
| NM_004570 | PIK3C2G | 984 | 1002 | a | u | a | C | A | U | A | U | U | u | U | U | A | U | U | G | A | U | A | -15 | 4 | 9 | bc | false | <90% | 4845 | ||
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_181504 | PIK3R1 | 213 | 231 | U | A | U | g | A | A | U | A | A | C | A | A | U | A | U | G | u | c | C | 37 | 3 | 12 | c | false | <90% | 5663 | ||
| NM_181524 | PIK3R1 | 373 | 391 | U | A | U | g | A | A | U | A | A | C | A | A | U | A | U | G | u | c | C | 37 | 3 | 12 | c | false | <90% | 5823 | ||
| NM_181523 | PIK3R1 | 1003 | 1021 | U | A | U | g | A | A | U | A | A | C | A | A | U | A | U | G | u | c | C | 37 | 3 | 12 | c | false | <90% | 6453 | ||
| NM_004984 | KIF5A | 3214 | 3232 | U | A | U | C | A | A | U | g | A | C | A | A | U | A | g | G | A | G | u | 8 | 3 | 7 | c | false | <90% | 3897 | ||
| NM_002690 | POLB | 944 | 962 | U | u | U | C | A | A | U | A | A | g | A | A | U | A | U | G | A | G | g | 0 | 3 | 8 | bc | false | <90% | 1259 | ||
| NM_002806 | PSMC6 | 1294 | 1312 | U | A | U | g | A | A | U | A | A | a | A | A | U | A | U | G | A | G | u | -24 | 3 | 8 | bc | false | <90% | 1590 | ||
3 prime UTR Seed matches
Hits to same gene : 0
Hits to other genes : 948
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