Automatic recommendation
OK - siRNA is specific for both sense and antisense (guide) strands
12 hits were found for CUGAUCAACACCAACGGCA (10 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_007252 | POU6F2 | 1225 | 1243 | g | U | G | A | U | C | A | A | C | A | C | C | c | A | g | G | G | C | A | 62 | 3 | 11 | false | <90% | 2223 | |||
| NM_017525 | CDC42BPG | 655 | 673 | C | g | u | c | U | C | A | A | C | A | C | C | A | A | C | G | G | C | A | 32 | 3 | 15 | bc | false | <90% | 4680 | ||
| NM_052820 | CORO2A | 641 | 659 | u | c | c | u | U | C | A | A | C | A | C | C | A | A | C | G | G | C | A | 30 | 4 | 15 | bc | false | <90% | 2265 | ||
| NM_003389 | CORO2A | 825 | 843 | u | c | c | u | U | C | A | A | C | A | C | C | A | A | C | G | G | C | A | 30 | 4 | 15 | bc | false | <90% | 2427 | ||
| XM_943417 | LOC648657 | 146 | 164 | a | U | c | A | U | C | A | u | C | A | C | C | A | A | C | G | G | C | A | 16 | 3 | 11 | bc | false | <90% | 1608 | ||
| XM_930991 | LOC642662 | 146 | 164 | a | U | c | A | U | C | A | u | C | A | C | C | A | A | C | G | G | C | A | 16 | 3 | 11 | bc | false | <90% | 1608 | ||
| XR_018464 | LOC139163 | 469 | 487 | g | U | G | A | U | C | A | A | C | A | g | C | A | A | C | G | u | C | A | 13 | 3 | 9 | c | false | <90% | 3846 | ||
| NM_000637 | GSR | 908 | 926 | a | U | G | A | U | C | A | g | C | A | C | C | A | A | C | u | G | C | A | 9 | 3 | 7 | c | false | <90% | 2262 | ||
| NM_001004726 | OR4X1 | 586 | 604 | C | U | G | A | U | C | A | u | C | A | C | C | A | A | u | G | G | C | g | 8 | 3 | 7 | c | false | <90% | 918 | ||
| NM_030961 | TRIM56 | 1945 | 1963 | C | U | c | A | U | C | A | A | C | c | C | C | A | A | C | G | G | C | g | -7 | 3 | 8 | bc | false | <90% | 3547 | ||
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_005509 | DMXL1 | 8876 | 8894 | a | G | C | C | G | U | U | G | c | U | G | U | U | G | A | U | C | c | a | 30 | 4 | 8 | c | false | <90% | 11072 | ||
| NM_000259 | MYO5A | 10547 | 10565 | U | G | C | C | G | U | a | G | G | U | G | U | U | G | A | U | g | g | G | 7 | 3 | 9 | c | false | <90% | 12227 | ||
3 prime UTR Seed matches
Hits to same gene : 0
Hits to other genes : 1565
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