Automatic recommendation
OK - siRNA is specific for both sense and antisense (guide) strands
11 hits were found for CCUGAUUGGCAUGCUACAG (1 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_002299 | LCT | 1448 | 1466 | g | C | U | G | A | U | U | G | a | C | A | g | G | C | U | A | C | A | G | 4 | 3 | 7 | false | <90% | 6274 | |||
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_024949 | WWC2 | 5889 | 5907 | C | U | G | U | A | G | C | A | U | G | C | a | A | A | U | C | A | a | a | 58 | 3 | 11 | false | <90% | 6492 | |||
| NM_178270 | ATG4A | 2013 | 2031 | C | U | G | U | A | G | C | u | U | G | C | C | A | A | U | C | A | G | u | 32 | 2 | 10 | bc | false | <90% | 2117 | ||
| NM_052936 | ATG4A | 2199 | 2217 | C | U | G | U | A | G | C | u | U | G | C | C | A | A | U | C | A | G | u | 32 | 2 | 10 | bc | false | <90% | 2303 | ||
| XR_018537 | LOC648977 | 1313 | 1331 | C | U | G | U | A | G | C | A | g | G | C | C | A | A | g | C | A | G | G | 15 | 2 | 8 | c | false | <90% | 1674 | ||
| XR_017372 | LOC342732 | 1313 | 1331 | C | U | G | U | A | G | C | A | g | G | C | C | A | A | g | C | A | G | G | 15 | 2 | 8 | c | false | <90% | 1674 | ||
| XM_940612 | DCAMKL3 | 4137 | 4155 | C | U | G | U | A | G | u | A | U | G | C | C | A | c | U | C | A | G | G | 14 | 2 | 6 | c | false | <90% | 5740 | ||
| XM_047355 | DCAMKL3 | 4144 | 4162 | C | U | G | U | A | G | u | A | U | G | C | C | A | c | U | C | A | G | G | 14 | 2 | 6 | c | false | <90% | 5747 | ||
| XR_019369 | LOC652524 | 1157 | 1175 | g | U | G | U | A | G | C | A | g | G | C | C | A | A | g | C | A | G | G | 13 | 3 | 7 | c | false | <90% | 1529 | ||
| XR_017099 | LOC126811 | 1157 | 1175 | g | U | G | U | A | G | C | A | g | G | C | C | A | A | g | C | A | G | G | 13 | 3 | 7 | c | false | <90% | 1529 | ||
| NM_005761 | PLXNC1 | 1920 | 1938 | C | U | G | U | A | G | C | A | U | c | C | C | A | A | c | C | A | G | a | -12 | 3 | 9 | c | false | <90% | 5121 | ||
3 prime UTR Seed matches
Hits to same gene : 0
Hits to other genes : 2046
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