Automatic recommendation
Not OK - siRNA is not specific
11 hits were found for GAAUGUUGGUGACCCAACU (9 guide strand hits and 2 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_001005242 | PKP2 | 2143 | 2161 | G | c | A | U | G | U | U | G | G | U | G | A | C | C | C | A | A | g | U | 85 | 2 | 15 | ac | false | <90% | 4299 | ||
| NM_004572 | PKP2 | 2275 | 2293 | G | c | A | U | G | U | U | G | G | U | G | A | C | C | C | A | A | g | U | 85 | 2 | 15 | ac | false | <90% | 4431 | ||
| NM_005915 | MCM6 | 1255 | 1273 | c | A | u | U | G | U | U | G | G | U | G | A | C | C | C | A | A | g | U | 75 | 3 | 14 | c | false | <90% | 3769 | ||
| NM_024939 | RBM35B | 2282 | 2300 | G | c | c | U | G | U | U | G | G | U | G | A | C | C | C | A | c | C | U | 45 | 3 | 13 | c | false | <90% | 4021 | ||
| NM_080544 | COLQ | 1303 | 1321 | G | A | A | U | G | U | U | G | c | U | G | A | C | C | C | A | g | g | c | 8 | 4 | 8 | c | false | <90% | 2523 | ||
| NM_080539 | COLQ | 1685 | 1703 | G | A | A | U | G | U | U | G | c | U | G | A | C | C | C | A | g | g | c | 8 | 4 | 8 | c | false | <90% | 2905 | ||
| NM_080541 | COLQ | 1760 | 1778 | G | A | A | U | G | U | U | G | c | U | G | A | C | C | C | A | g | g | c | 8 | 4 | 8 | c | false | <90% | 2980 | ||
| NM_005677 | COLQ | 1787 | 1805 | G | A | A | U | G | U | U | G | c | U | G | A | C | C | C | A | g | g | c | 8 | 4 | 8 | c | false | <90% | 3007 | ||
| NM_080538 | COLQ | 1916 | 1934 | G | A | A | U | G | U | U | G | c | U | G | A | C | C | C | A | g | g | c | 8 | 4 | 8 | c | false | <90% | 3136 | ||
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_017120 | LOC646090 | 1964 | 1982 | A | G | U | U | G | G | G | g | C | A | C | C | A | A | C | A | a | g | a | 6 | 4 | 8 | c | false | <90% | 2897 | ||
| NM_033103 | RHPN2 | 1958 | 1976 | A | G | U | U | G | G | G | g | C | A | C | C | A | A | C | A | a | g | a | 6 | 4 | 8 | c | false | <90% | 3516 | ||
3 prime UTR Seed matches
Hits to same gene : 0
Hits to other genes : 3069
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