Automatic recommendation
OK - siRNA is specific for both sense and antisense (guide) strands
11 hits were found for UGGCUGGAUCGAGUGAGCA (9 guide strand hits and 2 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_001001344 | ATP2B3 | 582 | 600 | U | G | G | C | U | G | G | A | U | C | G | A | G | g | G | g | G | C | u | 49 | 3 | 13 | c | false | <90% | 6438 | ||
| NM_021949 | ATP2B3 | 582 | 600 | U | G | G | C | U | G | G | A | U | C | G | A | G | g | G | g | G | C | u | 49 | 3 | 13 | c | false | <90% | 6592 | ||
| NM_153487 | MDGA1 | 2677 | 2695 | c | G | G | C | U | G | G | A | g | C | G | A | G | U | G | A | G | C | c | 32 | 3 | 9 | bc | false | <90% | 8907 | ||
| NM_152744 | SDK1 | 1053 | 1071 | U | G | G | C | U | G | G | A | U | C | c | A | G | U | G | A | G | a | c | 31 | 3 | 10 | c | false | <90% | 10397 | ||
| NM_024895 | PDZD7 | 1131 | 1149 | U | G | G | C | U | G | G | A | c | C | G | A | c | U | G | A | G | C | A | 29 | 2 | 8 | false | <90% | 2037 | |||
| NM_080918 | DGUOK | 7 | 25 | g | c | G | C | U | G | G | A | g | C | G | A | G | U | G | A | G | C | A | 26 | 3 | 10 | bc | false | <90% | 880 | ||
| NM_080916 | DGUOK | 7 | 25 | g | c | G | C | U | G | G | A | g | C | G | A | G | U | G | A | G | C | A | 26 | 3 | 10 | bc | false | <90% | 1144 | ||
| NM_025084 | FLJ22795 | 1298 | 1316 | U | G | G | C | U | G | G | c | U | g | G | A | G | U | G | A | G | C | g | -49 | 3 | 8 | bc | false | <90% | 2546 | ||
| XR_015455 | LOC388161 | 1517 | 1535 | U | G | G | C | U | G | G | c | U | g | G | A | G | U | G | A | G | C | g | -49 | 3 | 8 | bc | false | <90% | 5435 | ||
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_020640 | DCUN1D1 | 331 | 349 | c | u | g | g | C | A | C | U | C | G | A | U | C | C | A | G | C | C | A | 30 | 4 | 15 | bc | false | <90% | 3192 | ||
| NM_006959 | ZNF17 | 2457 | 2475 | U | c | C | U | C | A | C | U | C | c | A | U | C | C | A | G | C | C | u | 0 | 3 | 8 | bc | false | <90% | 2678 | ||
3 prime UTR Seed matches
Hits to same gene : 0
Hits to other genes : 3565
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