Automatic recommendation
OK - siRNA is specific for both sense and antisense (guide) strands
20 hits were found for GUGCACACAAUCCAGUGUG (16 guide strand hits and 4 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_002253 | KDR | 3544 | 3562 | G | U | G | u | A | C | A | C | A | A | U | C | C | A | G | a | G | U | G | 37 | 2 | 11 | c | false | <90% | 5830 | ||
| NM_002558 | P2RX1 | 2500 | 2518 | a | U | G | C | A | C | A | C | A | A | c | C | C | A | G | U | G | U | a | 31 | 3 | 9 | c | false | <90% | 2910 | ||
| XR_017828 | MYO15B | 717 | 735 | u | g | u | C | c | C | A | C | A | A | U | C | C | A | G | U | G | U | G | 15 | 4 | 14 | bc | false | <90% | 6012 | ||
| NM_001009942 | ANKRD16 | 657 | 675 | a | U | G | g | A | C | g | C | A | A | U | C | C | A | G | U | G | U | G | -5 | 3 | 12 | bc | false | <90% | 1069 | ||
| NM_001009943 | ANKRD16 | 657 | 675 | a | U | G | g | A | C | g | C | A | A | U | C | C | A | G | U | G | U | G | -5 | 3 | 12 | bc | false | <90% | 1095 | ||
| NM_001009941 | ANKRD16 | 657 | 675 | a | U | G | g | A | C | g | C | A | A | U | C | C | A | G | U | G | U | G | -5 | 3 | 12 | bc | false | <90% | 1174 | ||
| NM_019046 | ANKRD16 | 657 | 675 | a | U | G | g | A | C | g | C | A | A | U | C | C | A | G | U | G | U | G | -5 | 3 | 12 | bc | false | <90% | 2121 | ||
| NM_015354 | NUP188 | 4661 | 4679 | u | U | G | C | A | C | A | C | A | g | U | C | C | A | G | U | a | U | G | -8 | 3 | 8 | c | false | <90% | 5689 | ||
| NM_002252 | KCNS3 | 218 | 236 | c | a | c | C | A | C | A | C | A | u | U | C | C | A | G | U | G | U | G | -15 | 4 | 9 | bc | false | <90% | 2344 | ||
| XR_015528 | DKFZP434B061 | 209 | 227 | G | U | G | C | A | C | A | C | c | A | a | C | C | A | G | U | G | U | c | -26 | 3 | 8 | c | false | <90% | 997 | ||
| XM_001130267 | LOC729444 | 162 | 180 | G | U | G | C | A | C | A | C | c | A | a | C | C | A | G | U | G | U | a | -26 | 3 | 8 | c | false | <90% | 1055 | ||
| XR_015212 | LOC727962 | 200 | 218 | G | U | G | C | A | C | A | C | c | A | a | C | C | A | G | U | G | U | a | -26 | 3 | 8 | c | false | <90% | 1695 | ||
| XM_001130329 | LOC729461 | 200 | 218 | G | U | G | C | A | C | A | C | c | A | a | C | C | A | G | U | G | U | a | -26 | 3 | 8 | c | false | <90% | 1720 | ||
| XM_001126757 | FLJ26056 | 246 | 264 | G | U | G | C | A | C | A | C | c | A | a | C | C | A | G | U | G | U | a | -26 | 3 | 8 | c | false | <90% | 1870 | ||
| XM_931343 | LOC653135 | 317 | 335 | G | U | G | C | A | C | A | C | c | A | a | C | C | A | G | U | G | U | a | -26 | 3 | 8 | c | false | <90% | 3219 | ||
| XM_932721 | LOC653264 | 317 | 335 | G | U | G | C | A | C | A | C | c | A | a | C | C | A | G | U | G | U | a | -26 | 3 | 8 | c | false | <90% | 3220 | ||
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_014452 | TNFRSF21 | 2783 | 2801 | C | A | C | A | C | U | G | G | A | U | U | G | U | G | a | G | g | c | u | 44 | 4 | 14 | c | false | <90% | 3662 | ||
| NM_206828 | NLRP7 | 1169 | 1187 | u | g | u | g | C | U | G | G | A | U | U | G | U | G | U | G | C | A | C | 30 | 4 | 15 | bc | false | <90% | 3245 | ||
| NM_139176 | NLRP7 | 1169 | 1187 | u | g | u | g | C | U | G | G | A | U | U | G | U | G | U | G | C | A | C | 30 | 4 | 15 | bc | false | <90% | 3331 | ||
| NM_001004298 | C10orf90 | 756 | 774 | C | A | C | A | C | U | G | G | g | U | U | G | U | G | U | G | a | g | a | 8 | 4 | 8 | c | false | <90% | 3097 | ||
3 prime UTR Seed matches
Hits to same gene : 0
Hits to other genes : 1971
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