Automatic recommendation
OK - siRNA is specific for both sense and antisense (guide) strands
18 hits were found for GGACUAGAGGUUAGAGGAG (12 guide strand hits and 6 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_003983 | SLC7A6 | 1764 | 1782 | u | G | A | C | U | A | G | A | G | G | U | c | A | G | A | G | G | u | G | 61 | 3 | 10 | false | <90% | 6275 | |||
| NM_001076785 | SLC7A6 | 1851 | 1869 | u | G | A | C | U | A | G | A | G | G | U | c | A | G | A | G | G | u | G | 61 | 3 | 10 | false | <90% | 6362 | |||
| NM_020766 | PCDH19 | 3527 | 3545 | G | G | c | C | U | A | G | A | G | G | U | U | A | G | A | G | c | A | c | 51 | 3 | 13 | c | false | <90% | 6507 | ||
| XM_001132522 | LOC728689 | 282 | 300 | G | G | A | C | a | A | G | A | G | G | U | U | u | G | A | G | G | A | G | 38 | 2 | 7 | false | <90% | 2610 | |||
| XM_001132482 | LOC728689 | 248 | 266 | G | G | A | C | a | A | G | A | G | G | U | U | u | G | A | G | G | A | G | 38 | 2 | 7 | false | <90% | 3053 | |||
| NM_003752 | EIF3S8 | 247 | 265 | G | G | A | C | a | A | G | A | G | G | U | U | u | G | A | G | G | A | G | 38 | 2 | 7 | false | <90% | 3063 | |||
| XM_001132506 | LOC728689 | 296 | 314 | G | G | A | C | a | A | G | A | G | G | U | U | u | G | A | G | G | A | G | 38 | 2 | 7 | false | <90% | 3101 | |||
| NM_001037808 | EIF3S8 | 296 | 314 | G | G | A | C | a | A | G | A | G | G | U | U | u | G | A | G | G | A | G | 38 | 2 | 7 | false | <90% | 3111 | |||
| XM_001132509 | LOC728689 | 372 | 390 | G | G | A | C | a | A | G | A | G | G | U | U | u | G | A | G | G | A | G | 38 | 2 | 7 | false | <90% | 3177 | |||
| XM_001132505 | LOC728689 | 455 | 473 | G | G | A | C | a | A | G | A | G | G | U | U | u | G | A | G | G | A | G | 38 | 2 | 7 | false | <90% | 3260 | |||
| NM_006645 | STARD10 | 176 | 194 | G | G | A | C | a | A | c | A | G | G | U | U | A | G | A | G | G | A | a | -22 | 3 | 11 | bc | false | <90% | 1988 | ||
| NM_018237 | CCAR1 | 2378 | 2396 | G | G | A | C | U | A | c | A | G | a | U | U | A | G | A | G | G | A | u | -54 | 3 | 8 | bc | false | <90% | 3858 | ||
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_022459 | XPO4 | 6076 | 6094 | a | U | C | C | U | u | U | A | A | C | C | U | C | U | A | G | U | u | u | 27 | 4 | 11 | c | false | <90% | 8256 | ||
| NM_020223 | FAM20C | 526 | 544 | C | U | C | C | U | C | c | A | A | C | C | U | C | U | c | G | U | C | C | 9 | 2 | 7 | c | false | <90% | 2768 | ||
| XR_016003 | LOC732095 | 2350 | 2368 | C | U | C | C | U | C | U | c | A | C | C | U | C | U | A | G | a | g | a | 6 | 4 | 8 | c | false | <90% | 2583 | ||
| XR_015983 | LOC729799 | 2353 | 2371 | C | U | C | C | U | C | U | c | A | C | C | U | C | U | A | G | a | g | a | 6 | 4 | 8 | c | false | <90% | 2586 | ||
| NM_003003 | SEC14L1 | 2461 | 2479 | C | U | C | C | U | C | U | c | A | C | C | U | C | U | A | G | a | u | a | 6 | 4 | 8 | c | false | <90% | 2695 | ||
| NM_017919 | STX17 | 1842 | 1860 | C | U | C | C | U | a | U | A | A | C | C | U | C | U | A | G | g | u | a | 5 | 4 | 10 | c | false | <90% | 2678 | ||
3 prime UTR Seed matches
Hits to same gene : 0
Hits to other genes : 884
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