Automatic recommendation
OK - siRNA is specific for both sense and antisense (guide) strands
13 hits were found for GCACACACGUAGACAUUCG (4 guide strand hits and 9 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_138318 | KCNK10 | 2061 | 2079 | G | C | A | C | A | C | A | C | G | U | A | G | A | C | A | a | g | g | G | 47 | 3 | 15 | c | false | <90% | 2401 | ||
| NM_138317 | KCNK10 | 2144 | 2162 | G | C | A | C | A | C | A | C | G | U | A | G | A | C | A | a | g | g | G | 47 | 3 | 15 | c | false | <90% | 2484 | ||
| NM_021161 | KCNK10 | 2378 | 2396 | G | C | A | C | A | C | A | C | G | U | A | G | A | C | A | a | g | g | G | 47 | 3 | 15 | c | false | <90% | 2710 | ||
| NR_003051 | RMRP | 106 | 124 | a | u | A | C | g | C | A | C | G | U | A | G | A | C | A | U | U | C | c | 30 | 4 | 13 | bc | false | <90% | 265 | ||
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 | |||||||||||||
| XM_001132528 | NPTX1 | 2747 | 2765 | u | G | u | g | U | G | U | C | U | A | C | G | U | G | U | G | U | G | C | 41 | 3 | 15 | bc | false | <90% | 4653 | ||
| NM_002522 | NPTX1 | 1780 | 1798 | u | G | u | g | U | G | U | C | U | A | C | G | U | G | U | G | U | G | C | 41 | 3 | 15 | bc | false | <90% | 5441 | ||
| NM_004711 | SYNGR1 | 930 | 948 | g | G | A | c | U | G | U | C | U | A | C | G | U | a | U | G | U | G | C | 41 | 3 | 9 | c | false | <90% | 4425 | ||
| NM_017772 | TBC1D22B | 1469 | 1487 | u | u | c | A | U | c | U | C | U | A | C | G | U | G | U | G | U | G | C | 3 | 4 | 13 | bc | false | <90% | 3477 | ||
| NM_025090 | USP36 | 1217 | 1235 | a | G | A | A | U | G | c | C | U | A | C | a | U | G | U | G | U | G | C | -2 | 3 | 7 | false | <90% | 5234 | |||
| NM_178221 | ATG4C | 32 | 50 | g | G | A | A | c | G | U | C | U | g | C | G | U | G | U | G | U | G | C | -36 | 3 | 9 | bc | false | <90% | 1774 | ||
| NM_032852 | ATG4C | 32 | 50 | g | G | A | A | c | G | U | C | U | g | C | G | U | G | U | G | U | G | C | -36 | 3 | 9 | bc | false | <90% | 1822 | ||
| XM_001134374 | LOC730132 | 985 | 1003 | u | G | A | A | U | G | U | g | U | g | C | G | U | G | U | G | U | G | C | -46 | 3 | 9 | bc | false | <90% | 2247 | ||
| XM_001134027 | LOC731889 | 985 | 1003 | u | G | A | A | U | G | U | g | U | g | C | G | U | G | U | G | U | G | C | -46 | 3 | 9 | bc | false | <90% | 2247 | ||
3 prime UTR Seed matches
Hits to same gene : 0
Hits to other genes : 2361
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)
Motif found in sense strand
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