Automatic recommendation
OK - siRNA is specific for both sense and antisense (guide) strands
18 hits were found for GGAUGUGGACUUUUCGGGA (4 guide strand hits and 14 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_003129 | SQLE | 925 | 943 | c | c | A | U | G | U | G | G | A | C | U | U | U | U | C | u | G | G | g | 55 | 4 | 13 | c | false | <90% | 2989 | ||
| XM_001132928 | LOC728969 | 3812 | 3830 | G | G | c | U | G | U | G | a | A | C | U | U | U | U | C | G | G | G | A | 18 | 2 | 11 | bc | false | <90% | 4055 | ||
| NM_194317 | LYPD6 | 1084 | 1102 | a | G | A | U | G | U | G | G | g | C | U | U | U | U | C | a | G | G | A | 11 | 3 | 7 | c | false | <90% | 3501 | ||
| NM_014787 | DNAJC6 | 1649 | 1667 | G | G | A | U | G | U | G | G | A | C | c | U | U | U | u | G | G | G | c | 9 | 3 | 10 | c | false | <90% | 5750 | ||
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_004023 | DMD | 1627 | 1645 | a | C | C | a | G | A | A | A | A | G | U | C | C | A | C | A | U | g | a | 53 | 4 | 13 | c | false | <90% | 7048 | ||
| NM_004020 | DMD | 1627 | 1645 | a | C | C | a | G | A | A | A | A | G | U | C | C | A | C | A | U | g | a | 53 | 4 | 13 | c | false | <90% | 7050 | ||
| NM_004022 | DMD | 1627 | 1645 | a | C | C | a | G | A | A | A | A | G | U | C | C | A | C | A | U | g | a | 53 | 4 | 13 | c | false | <90% | 7339 | ||
| NM_004021 | DMD | 1627 | 1645 | a | C | C | a | G | A | A | A | A | G | U | C | C | A | C | A | U | g | a | 53 | 4 | 13 | c | false | <90% | 7378 | ||
| NM_004013 | DMD | 1627 | 1645 | a | C | C | a | G | A | A | A | A | G | U | C | C | A | C | A | U | g | a | 53 | 4 | 13 | c | false | <90% | 7410 | ||
| NM_004011 | DMD | 3990 | 4008 | a | C | C | a | G | A | A | A | A | G | U | C | C | A | C | A | U | g | a | 53 | 4 | 13 | c | false | <90% | 9773 | ||
| NM_004012 | DMD | 4133 | 4151 | a | C | C | a | G | A | A | A | A | G | U | C | C | A | C | A | U | g | a | 53 | 4 | 13 | c | false | <90% | 9916 | ||
| NM_004007 | DMD | 7981 | 7999 | a | C | C | a | G | A | A | A | A | G | U | C | C | A | C | A | U | g | a | 53 | 4 | 13 | c | false | <90% | 13764 | ||
| NM_004006 | DMD | 8210 | 8228 | a | C | C | a | G | A | A | A | A | G | U | C | C | A | C | A | U | g | a | 53 | 4 | 13 | c | false | <90% | 13993 | ||
| NM_004009 | DMD | 8217 | 8235 | a | C | C | a | G | A | A | A | A | G | U | C | C | A | C | A | U | g | a | 53 | 4 | 13 | c | false | <90% | 14000 | ||
| NM_000109 | DMD | 8286 | 8304 | a | C | C | a | G | A | A | A | A | G | U | C | C | A | C | A | U | g | a | 53 | 4 | 13 | c | false | <90% | 14069 | ||
| NM_004010 | DMD | 8299 | 8317 | a | C | C | a | G | A | A | A | A | G | U | C | C | A | C | A | U | g | a | 53 | 4 | 13 | c | false | <90% | 14082 | ||
| NM_052911 | ESCO1 | 1762 | 1780 | U | C | C | C | a | A | A | A | A | G | U | C | C | A | C | A | g | C | C | 25 | 2 | 11 | c | false | <90% | 4499 | ||
| NM_001235 | SERPINH1 | 1701 | 1719 | g | C | C | C | G | g | A | A | A | c | U | C | C | A | C | A | U | C | C | -48 | 3 | 9 | bc | false | <90% | 2208 | ||
3 prime UTR Seed matches
Hits to same gene : 0
Hits to other genes : 2222
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