Automatic recommendation
OK - siRNA is specific for both sense and antisense (guide) strands
23 hits were found for GCAGGAAGCAGCUAACAUA (22 guide strand hits and 1 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_016584 | IL23A | 7 | 25 | a | C | A | G | G | A | A | G | C | A | G | C | U | u | A | C | A | a | A | 75 | 3 | 12 | c | false | <90% | 1049 | ||
| NM_144490 | AKAP11 | 4315 | 4333 | a | C | A | G | G | A | A | G | C | A | G | C | U | A | A | g | A | c | A | 69 | 3 | 14 | c | false | <90% | 5947 | ||
| NM_016248 | AKAP11 | 4315 | 4333 | a | C | A | G | G | A | A | G | C | A | G | C | U | A | A | g | A | c | A | 69 | 3 | 14 | c | false | <90% | 9919 | ||
| NM_152468 | TMC8 | 1140 | 1158 | G | C | A | G | G | A | A | G | C | A | G | C | c | A | c | C | A | U | c | 59 | 3 | 12 | false | <90% | 2798 | |||
| XM_001132951 | LOC339535 | 354 | 372 | u | C | A | G | G | A | A | G | C | A | G | u | U | A | A | C | A | c | u | 56 | 4 | 10 | false | <90% | 1559 | |||
| XM_001132766 | LOC339535 | 354 | 372 | u | C | A | G | G | A | A | G | C | A | G | u | U | A | A | C | A | c | u | 56 | 4 | 10 | false | <90% | 1559 | |||
| NM_020242 | KIF15 | 919 | 937 | G | a | A | G | G | A | A | G | C | A | G | g | U | A | A | C | A | U | A | 54 | 2 | 9 | false | <90% | 4775 | |||
| NM_138350 | THAP3 | 77 | 95 | G | C | A | G | G | A | A | G | C | A | G | C | U | c | A | C | c | U | u | 51 | 3 | 13 | c | false | <90% | 2052 | ||
| NM_004023 | DMD | 342 | 360 | G | g | A | G | G | A | A | G | C | A | G | a | U | A | A | C | A | U | u | 49 | 3 | 9 | false | <90% | 7048 | |||
| NM_004020 | DMD | 342 | 360 | G | g | A | G | G | A | A | G | C | A | G | a | U | A | A | C | A | U | u | 49 | 3 | 9 | false | <90% | 7050 | |||
| NM_004022 | DMD | 342 | 360 | G | g | A | G | G | A | A | G | C | A | G | a | U | A | A | C | A | U | u | 49 | 3 | 9 | false | <90% | 7339 | |||
| NM_004021 | DMD | 342 | 360 | G | g | A | G | G | A | A | G | C | A | G | a | U | A | A | C | A | U | u | 49 | 3 | 9 | false | <90% | 7378 | |||
| NM_004013 | DMD | 342 | 360 | G | g | A | G | G | A | A | G | C | A | G | a | U | A | A | C | A | U | u | 49 | 3 | 9 | false | <90% | 7410 | |||
| NM_004011 | DMD | 2705 | 2723 | G | g | A | G | G | A | A | G | C | A | G | a | U | A | A | C | A | U | u | 49 | 3 | 9 | false | <90% | 9773 | |||
| NM_004012 | DMD | 2848 | 2866 | G | g | A | G | G | A | A | G | C | A | G | a | U | A | A | C | A | U | u | 49 | 3 | 9 | false | <90% | 9916 | |||
| NM_004007 | DMD | 6696 | 6714 | G | g | A | G | G | A | A | G | C | A | G | a | U | A | A | C | A | U | u | 49 | 3 | 9 | false | <90% | 13764 | |||
| NM_004006 | DMD | 6925 | 6943 | G | g | A | G | G | A | A | G | C | A | G | a | U | A | A | C | A | U | u | 49 | 3 | 9 | false | <90% | 13993 | |||
| NM_004009 | DMD | 6932 | 6950 | G | g | A | G | G | A | A | G | C | A | G | a | U | A | A | C | A | U | u | 49 | 3 | 9 | false | <90% | 14000 | |||
| NM_000109 | DMD | 7001 | 7019 | G | g | A | G | G | A | A | G | C | A | G | a | U | A | A | C | A | U | u | 49 | 3 | 9 | false | <90% | 14069 | |||
| NM_004010 | DMD | 7014 | 7032 | G | g | A | G | G | A | A | G | C | A | G | a | U | A | A | C | A | U | u | 49 | 3 | 9 | false | <90% | 14082 | |||
| NM_007126 | VCP | 838 | 856 | G | C | A | G | G | A | A | G | C | A | G | C | U | A | g | C | u | c | A | 49 | 3 | 14 | c | false | <90% | 3198 | ||
| NM_001369 | DNAH5 | 609 | 627 | u | C | A | G | G | A | c | G | C | A | G | C | U | A | A | C | A | U | u | 26 | 3 | 11 | bc | false | <90% | 13971 | ||
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_002265 | KPNB1 | 1640 | 1658 | U | u | U | G | U | g | A | G | C | U | G | C | U | U | C | C | U | G | a | 20 | 3 | 12 | bc | false | <90% | 4205 | ||
3 prime UTR Seed matches
Hits to same gene : 0
Hits to other genes : 2697
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