Automatic recommendation
OK - siRNA is specific for both sense and antisense (guide) strands
11 hits were found for GAGGUAUAUGACUUUGCUU (6 guide strand hits and 5 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_020871 | LRCH2 | 1235 | 1253 | G | A | G | G | U | A | U | A | U | G | A | u | U | U | U | G | u | U | g | 37 | 3 | 11 | false | <90% | 4943 | |||
| XM_001131352 | CRTAP | 860 | 878 | G | A | G | c | U | g | U | A | U | G | A | C | U | U | U | G | C | U | a | -5 | 3 | 12 | bc | false | <90% | 1691 | ||
| NM_014269 | ADAM29 | 1004 | 1022 | c | A | G | a | U | A | a | A | U | G | A | C | U | U | U | G | C | U | U | -5 | 3 | 12 | bc | false | <90% | 3282 | ||
| NM_006371 | CRTAP | 1199 | 1217 | G | A | G | c | U | g | U | A | U | G | A | C | U | U | U | G | C | U | a | -5 | 3 | 12 | bc | false | <90% | 6622 | ||
| NM_016029 | DHRS7 | 1208 | 1226 | a | A | u | a | g | A | U | A | U | G | A | C | U | U | U | G | C | U | U | -9 | 4 | 14 | bc | false | <90% | 1282 | ||
| XM_001126406 | LOC727922 | 1626 | 1644 | u | A | G | G | U | A | a | A | U | a | A | C | U | U | U | G | C | U | U | -51 | 3 | 9 | bc | false | <90% | 8861 | ||
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 | |||||||||||||
| XR_017614 | LOC645688 | 1812 | 1830 | g | A | u | C | A | A | A | G | U | C | A | U | A | U | A | C | C | U | g | 73 | 3 | 15 | bc | false | <90% | 2338 | ||
| XR_019524 | LOC645688 | 1812 | 1830 | g | A | u | C | A | A | A | G | U | C | A | U | A | U | A | C | C | U | g | 73 | 3 | 15 | bc | false | <90% | 2338 | ||
| NM_015346 | ZFYVE26 | 6966 | 6984 | A | A | G | C | A | A | A | G | U | C | A | U | A | U | A | C | a | g | a | 68 | 3 | 16 | ac | false | <90% | 9688 | ||
| XR_019130 | RPL12P6 | 39 | 57 | A | A | u | C | A | A | A | G | U | C | g | U | A | U | A | C | C | U | g | 14 | 3 | 7 | c | false | <90% | 564 | ||
| XR_016704 | RPL12P6 | 39 | 57 | A | A | u | C | A | A | A | G | U | C | g | U | A | U | A | C | C | U | g | 14 | 3 | 7 | c | false | <90% | 564 | ||
3 prime UTR Seed matches
Hits to same gene : 0
Hits to other genes : 1012
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