Automatic recommendation
OK - siRNA is specific for both sense and antisense (guide) strands
22 hits were found for AGAAUUUGGAGCUACUGUG (12 guide strand hits and 10 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 | |||||||||||||
| XM_927830 | LOC644732 | 378 | 396 | u | G | g | A | U | U | U | G | G | A | G | C | c | A | C | U | G | U | G | 68 | 3 | 9 | false | <90% | 3234 | |||
| NM_000052 | ATP7A | 1781 | 1799 | u | G | g | A | U | U | U | G | G | A | G | C | c | A | C | U | G | U | G | 68 | 3 | 9 | false | <90% | 8122 | |||
| NM_005072 | SLC12A4 | 654 | 672 | A | G | A | A | U | U | U | G | G | A | G | g | U | g | C | U | G | U | G | 46 | 2 | 11 | false | <90% | 3884 | |||
| NM_003875 | GMPS | 671 | 689 | g | G | u | A | U | U | U | G | G | A | G | g | U | A | C | U | G | U | G | 44 | 3 | 8 | false | <90% | 2457 | |||
| NM_006345 | SLC30A9 | 1834 | 1852 | u | a | g | A | U | U | U | G | G | A | G | a | U | A | C | U | G | U | G | 33 | 4 | 8 | false | <90% | 3272 | |||
| NM_002238 | KCNH1 | 1205 | 1223 | u | G | A | A | U | a | U | G | G | A | G | C | U | g | C | U | G | U | G | 15 | 3 | 7 | c | false | <90% | 3127 | ||
| NM_172362 | KCNH1 | 1286 | 1304 | u | G | A | A | U | a | U | G | G | A | G | C | U | g | C | U | G | U | G | 15 | 3 | 7 | c | false | <90% | 3208 | ||
| NM_002478 | MYOD1 | 216 | 234 | A | G | g | A | U | a | U | G | G | A | G | C | U | A | C | U | G | U | c | 12 | 3 | 12 | bc | false | <90% | 1823 | ||
| XR_019515 | LOC339858 | 158 | 176 | A | G | A | A | U | g | U | G | G | A | a | C | U | A | C | U | G | U | u | -29 | 3 | 7 | c | false | <90% | 574 | ||
| XR_017649 | LOC339858 | 158 | 176 | A | G | A | A | U | g | U | G | G | A | a | C | U | A | C | U | G | U | u | -29 | 3 | 7 | c | false | <90% | 574 | ||
| NM_001859 | SLC31A1 | 281 | 299 | A | G | A | A | U | g | U | G | G | A | a | C | U | A | C | U | G | U | u | -29 | 3 | 7 | c | false | <90% | 4735 | ||
| NM_017711 | GDPD2 | 995 | 1013 | u | G | A | A | U | g | c | G | G | A | G | C | U | A | C | U | G | U | G | -31 | 3 | 12 | bc | false | <90% | 2199 | ||
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_080740 | SUHW1 | 2033 | 2051 | a | g | a | A | G | U | A | G | C | U | C | C | A | A | A | g | U | C | U | 40 | 4 | 12 | c | false | <90% | 2180 | ||
| NM_001005180 | OR56B1 | 33 | 51 | u | c | C | A | a | U | A | G | C | U | C | C | A | A | A | U | U | C | c | 30 | 4 | 13 | bc | false | <90% | 975 | ||
| XM_940659 | LOC440338 | 2497 | 2515 | C | A | a | A | G | U | A | u | C | U | C | C | A | A | A | U | U | C | a | 13 | 3 | 10 | bc | false | <90% | 3853 | ||
| XM_496115 | LOC440338 | 2497 | 2515 | C | A | a | A | G | U | A | u | C | U | C | C | A | A | A | U | U | C | a | 13 | 3 | 10 | bc | false | <90% | 3853 | ||
| NM_014682 | ST18 | 1296 | 1314 | g | A | C | A | G | U | g | G | C | U | C | C | A | A | c | U | U | C | U | 6 | 3 | 7 | c | false | <90% | 6183 | ||
| NM_020863 | ZFAT1 | 852 | 870 | a | A | C | A | G | g | A | G | C | U | a | C | A | A | A | U | U | C | U | -26 | 3 | 8 | c | false | <90% | 4621 | ||
| NM_001029939 | ZFAT1 | 779 | 797 | a | A | C | A | G | g | A | G | C | U | a | C | A | A | A | U | U | C | U | -26 | 3 | 8 | c | false | <90% | 5469 | ||
| NM_001683 | ATP2B2 | 2803 | 2821 | g | A | C | A | G | c | A | u | C | U | C | C | A | A | A | U | U | C | U | -27 | 3 | 11 | bc | false | <90% | 6686 | ||
| NM_001001331 | ATP2B2 | 2938 | 2956 | g | A | C | A | G | c | A | u | C | U | C | C | A | A | A | U | U | C | U | -27 | 3 | 11 | bc | false | <90% | 6821 | ||
| NM_012115 | CASP8AP2 | 6187 | 6205 | C | A | C | A | G | a | A | G | C | U | u | C | A | A | A | U | U | C | c | -29 | 3 | 7 | c | false | <90% | 6782 | ||
3 prime UTR Seed matches
Hits to same gene : 0
Hits to other genes : 4313
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