Automatic recommendation
OK - siRNA is specific for both sense and antisense (guide) strands
20 hits were found for UAGAGAUCAUGACCUUGAU (10 guide strand hits and 10 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_002622 | PFDN1 | 177 | 195 | c | A | G | A | G | A | U | C | A | U | G | A | C | u | U | U | G | g | U | 75 | 3 | 12 | c | false | <90% | 1324 | ||
| NM_025134 | CHD9 | 1502 | 1520 | U | u | u | A | G | A | U | C | A | U | G | A | C | C | U | U | G | A | U | 69 | 2 | 16 | bc | false | <90% | 11479 | ||
| NM_012454 | TIAM2 | 3024 | 3042 | a | u | G | A | G | A | U | C | A | U | G | A | C | C | U | U | a | A | a | 58 | 4 | 14 | ac | false | <90% | 5916 | ||
| XM_942361 | LOC652733 | 357 | 375 | g | c | G | A | G | A | U | C | A | U | G | A | C | C | U | a | G | A | g | 55 | 4 | 13 | c | false | <90% | 483 | ||
| NM_031292 | PUS7L | 2041 | 2059 | g | g | a | A | G | A | U | C | A | U | G | A | C | a | U | U | G | A | U | 47 | 4 | 10 | c | false | <90% | 3959 | ||
| XM_001124973 | C10orf64 | 1384 | 1402 | U | A | G | A | G | A | U | C | A | U | G | c | C | C | c | U | G | A | a | 36 | 3 | 11 | false | <90% | 3472 | |||
| XM_001124974 | C10orf64 | 1384 | 1402 | U | A | G | A | G | A | U | C | A | U | G | c | C | C | c | U | G | A | a | 36 | 3 | 11 | false | <90% | 3472 | |||
| NM_054013 | MGAT4B | 14 | 32 | g | c | c | u | G | A | U | C | A | U | G | A | C | C | U | U | G | A | U | 30 | 4 | 15 | bc | false | <90% | 3592 | ||
| NM_201348 | PRELP | 3678 | 3696 | g | A | G | A | G | g | U | C | A | U | u | A | C | C | U | U | G | A | U | -26 | 3 | 8 | c | false | <90% | 5823 | ||
| NM_002725 | PRELP | 3688 | 3706 | g | A | G | A | G | g | U | C | A | U | u | A | C | C | U | U | G | A | U | -26 | 3 | 8 | c | false | <90% | 5833 | ||
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 | |||||||||||||
| XR_017002 | LOC220077 | 635 | 653 | g | a | C | A | A | G | G | U | C | A | U | G | u | U | C | U | C | U | u | 71 | 4 | 10 | false | <90% | 1442 | |||
| XR_019008 | LOC220077 | 635 | 653 | g | a | C | A | A | G | G | U | C | A | U | G | u | U | C | U | C | U | u | 71 | 4 | 10 | false | <90% | 1442 | |||
| NM_001381 | DOK1 | 658 | 676 | g | a | C | A | A | G | G | U | C | A | U | G | u | U | C | U | C | U | u | 71 | 4 | 10 | false | <90% | 1908 | |||
| NM_001039580 | MAP9 | 2977 | 2995 | u | U | C | A | A | G | G | U | C | A | U | u | A | U | C | a | C | U | A | 38 | 3 | 10 | false | <90% | 7333 | |||
| NM_001433 | ERN1 | 2199 | 2217 | A | U | C | A | A | G | G | c | C | A | U | G | A | U | C | U | C | c | g | 30 | 3 | 9 | c | false | <90% | 3620 | ||
| NM_000173 | GP1BA | 831 | 849 | g | U | C | A | A | G | G | c | C | A | U | G | A | c | C | U | C | U | A | 16 | 3 | 6 | c | false | <90% | 2427 | ||
| NM_032186 | ZNF644 | 207 | 225 | A | U | C | A | A | G | G | U | C | A | a | G | A | U | C | U | g | g | A | 12 | 3 | 10 | c | false | <90% | 2004 | ||
| NM_016620 | ZNF644 | 283 | 301 | A | U | C | A | A | G | G | U | C | A | a | G | A | U | C | U | g | g | A | 12 | 3 | 10 | c | false | <90% | 2085 | ||
| NM_201269 | ZNF644 | 3851 | 3869 | A | U | C | A | A | G | G | U | C | A | a | G | A | U | C | U | g | g | A | 12 | 3 | 10 | c | false | <90% | 5648 | ||
| NM_006218 | PIK3CA | 2632 | 2650 | A | U | C | A | A | G | G | U | C | u | U | G | A | U | C | U | u | c | g | -13 | 4 | 9 | c | false | <90% | 3724 | ||
3 prime UTR Seed matches
Hits to same gene : 0
Hits to other genes : 2197
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