Automatic recommendation
OK - siRNA is specific for both sense and antisense (guide) strands
15 hits were found for CUCCACCAUAGAUCACUCC (0 guide strand hits and 15 sense strand hits.)
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_030955 | ADAMTS12 | 1566 | 1584 | G | G | A | G | U | G | A | U | C | U | A | U | G | a | U | G | u | u | c | 49 | 4 | 13 | c | false | <90% | 4955 | ||
| NM_006571 | DCTN6 | 512 | 530 | a | c | g | G | U | G | A | U | C | U | A | U | G | G | U | G | c | A | G | 43 | 4 | 13 | c | false | <90% | 1044 | ||
| NM_006306 | SMC1A | 2018 | 2036 | G | G | A | G | U | G | A | U | C | U | c | U | G | G | U | G | G | g | G | 36 | 2 | 10 | c | false | <90% | 9725 | ||
| NM_080873 | ASB11 | 157 | 175 | G | a | A | G | a | G | A | U | C | U | A | U | G | G | U | G | G | A | a | 32 | 3 | 13 | bc | false | <90% | 972 | ||
| NM_020148 | SPIRE1 | 1271 | 1289 | G | G | A | G | U | c | A | U | C | U | A | U | G | G | U | G | a | A | u | 8 | 3 | 10 | c | false | <90% | 5402 | ||
| NM_001079882 | PRKD2 | 1766 | 1784 | G | G | A | G | U | G | g | U | C | U | A | U | G | G | a | G | G | A | a | 4 | 3 | 7 | c | false | <90% | 2939 | ||
| NM_001079881 | PRKD2 | 2029 | 2047 | G | G | A | G | U | G | g | U | C | U | A | U | G | G | a | G | G | A | a | 4 | 3 | 7 | c | false | <90% | 3202 | ||
| NM_001079880 | PRKD2 | 2165 | 2183 | G | G | A | G | U | G | g | U | C | U | A | U | G | G | a | G | G | A | a | 4 | 3 | 7 | c | false | <90% | 3338 | ||
| NM_016457 | PRKD2 | 2444 | 2462 | G | G | A | G | U | G | g | U | C | U | A | U | G | G | a | G | G | A | a | 4 | 3 | 7 | c | false | <90% | 3617 | ||
| NM_006096 | NDRG1 | 1453 | 1471 | a | G | A | G | U | G | A | g | C | U | c | U | G | G | U | G | G | A | G | -25 | 3 | 8 | c | false | <90% | 3074 | ||
| NM_004784 | NDST3 | 1581 | 1599 | u | G | A | G | U | c | A | U | C | U | u | U | G | G | U | G | G | A | G | -26 | 3 | 8 | c | false | <90% | 3188 | ||
| NM_212535 | PRKCB1 | 1328 | 1346 | G | G | A | G | U | G | c | a | C | U | A | U | G | G | U | G | G | A | G | -28 | 2 | 11 | bc | false | <90% | 2319 | ||
| NM_002738 | PRKCB1 | 1328 | 1346 | G | G | A | G | U | G | c | a | C | U | A | U | G | G | U | G | G | A | G | -28 | 2 | 11 | bc | false | <90% | 3411 | ||
| NM_144669 | GLT1D1 | 281 | 299 | G | G | A | G | U | c | A | U | C | U | u | U | G | G | U | G | G | A | a | -29 | 3 | 7 | c | false | <90% | 2721 | ||
| NM_030623 | SKIP | 3178 | 3196 | G | G | A | G | U | u | c | U | C | U | A | U | G | G | U | G | G | A | c | -34 | 3 | 11 | bc | false | <90% | 6824 | ||
3 prime UTR Seed matches
Hits to same gene : 0
Hits to other genes : 3197
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