Automatic recommendation
Not OK - siRNA is not specific
9 hits were found for GAAGUACUCUCUGACAACA (4 guide strand hits and 5 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_024560 | FLJ21963 | 1324 | 1342 | G | c | A | G | U | A | C | U | C | U | C | U | G | A | C | A | A | g | g | 80 | 3 | 15 | ac | false | <90% | 3033 | ||
| XM_001132204 | LOC732019 | 727 | 745 | u | u | u | G | a | A | C | U | C | U | C | U | G | A | C | A | A | C | A | 15 | 4 | 14 | bc | false | <90% | 1405 | ||
| NM_053043 | PRR8 | 166 | 184 | u | u | u | G | a | A | C | U | C | U | C | U | G | A | C | A | A | C | A | 15 | 4 | 14 | bc | false | <90% | 4382 | ||
| NM_002290 | LAMA4 | 1873 | 1891 | u | g | c | G | g | A | C | U | C | U | C | U | G | A | C | A | A | C | A | 15 | 4 | 14 | bc | false | <90% | 6297 | ||
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_004171 | SLC1A2 | 8069 | 8087 | U | G | U | U | G | U | C | A | G | A | G | A | a | g | A | C | U | U | C | 70 | 2 | 12 | false | <90% | 12021 | |||
| NM_024772 | ZMYM1 | 304 | 322 | U | G | U | U | u | U | C | A | G | A | G | A | G | U | g | C | U | U | C | 23 | 2 | 9 | c | false | <90% | 4172 | ||
| XR_017794 | LOC572558 | 429 | 447 | U | G | U | U | G | U | C | A | a | A | G | A | G | U | A | C | a | a | u | 8 | 4 | 8 | c | false | <90% | 609 | ||
| NM_144997 | FLCN | 1431 | 1449 | U | G | U | U | G | c | C | A | G | A | G | A | G | U | A | C | a | g | a | 5 | 4 | 10 | c | false | <90% | 3717 | ||
| NM_000944 | PPP3CA | 764 | 782 | U | G | U | U | G | a | C | A | G | A | G | g | G | U | A | C | U | U | C | 2 | 2 | 7 | false | <90% | 4424 | |||
3 prime UTR Seed matches
Hits to same gene : 0
Hits to other genes : 1009
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