Automatic recommendation
OK - siRNA is specific for both sense and antisense (guide) strands
11 hits were found for GGACCCACGGUGGAACAGG (2 guide strand hits and 9 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_004385 | VCAN | 7293 | 7311 | G | G | A | C | C | C | A | C | G | G | U | G | G | c | A | C | c | u | c | 49 | 4 | 13 | c | false | <90% | 11185 | ||
| NM_178457 | C20orf174 | 2164 | 2182 | c | G | A | C | C | C | A | g | G | G | U | G | G | A | A | g | A | G | G | 9 | 3 | 7 | c | false | <90% | 9404 | ||
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_197965 | SLC10A6 | 389 | 407 | C | C | U | G | U | U | C | C | A | C | C | G | U | G | G | c | c | g | C | 47 | 3 | 15 | c | false | <90% | 1134 | ||
| NM_001186 | BACH1 | 3214 | 3232 | a | u | U | u | U | U | C | C | A | C | C | G | U | G | G | G | U | C | a | 44 | 4 | 14 | bc | false | <90% | 5642 | ||
| NM_206866 | BACH1 | 3342 | 3360 | a | u | U | u | U | U | C | C | A | C | C | G | U | G | G | G | U | C | a | 44 | 4 | 14 | bc | false | <90% | 5770 | ||
| NM_020870 | SH3RF1 | 2780 | 2798 | C | C | U | G | U | U | C | C | u | C | C | c | U | G | G | G | U | C | C | 6 | 2 | 8 | false | <90% | 5265 | |||
| NM_080682 | VCAM1 | 854 | 872 | C | C | U | G | U | U | C | C | A | g | C | G | a | G | G | G | U | C | u | 1 | 3 | 9 | false | <90% | 2843 | |||
| NM_001078 | VCAM1 | 854 | 872 | C | C | U | G | U | U | C | C | A | g | C | G | a | G | G | G | U | C | u | 1 | 3 | 9 | false | <90% | 3119 | |||
| NM_203382 | AMACR | 1737 | 1755 | C | C | U | G | U | U | u | C | c | C | C | G | U | G | G | G | U | C | u | -31 | 3 | 9 | bc | false | <90% | 2373 | ||
| NM_014324 | AMACR | 1898 | 1916 | C | C | U | G | U | U | u | C | c | C | C | G | U | G | G | G | U | C | u | -31 | 3 | 9 | bc | false | <90% | 2534 | ||
| XM_940875 | LOC651672 | 838 | 856 | C | C | U | G | c | U | C | C | A | u | C | G | U | G | G | G | U | C | a | -39 | 3 | 8 | bc | false | <90% | 1287 | ||
3 prime UTR Seed matches
Hits to same gene : 0
Hits to other genes : 1913
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