Automatic recommendation
OK - siRNA is specific for both sense and antisense (guide) strands
12 hits were found for ACAUUGCUAUGAGCAAUUA (5 guide strand hits and 7 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_014892 | RBM16 | 975 | 993 | c | C | A | c | U | G | C | U | A | U | G | A | G | C | A | A | U | a | c | 53 | 4 | 13 | c | false | <90% | 5018 | ||
| NM_014585 | SLC40A1 | 3297 | 3315 | A | C | g | U | U | G | C | U | A | U | G | A | G | C | A | c | U | U | u | 49 | 3 | 12 | c | false | <90% | 3457 | ||
| NM_032890 | DISP1 | 146 | 164 | g | C | A | U | g | G | C | U | A | U | G | A | G | C | A | A | U | g | g | 38 | 4 | 12 | c | false | <90% | 4743 | ||
| NM_012262 | HS2ST1 | 6354 | 6372 | u | C | A | U | U | G | C | U | u | U | G | A | G | C | A | A | U | g | c | 30 | 4 | 8 | c | false | <90% | 6708 | ||
| NM_012259 | HEY2 | 1874 | 1892 | g | C | A | U | U | G | g | U | A | U | a | A | G | C | A | A | U | U | A | -29 | 3 | 8 | c | false | <90% | 2672 | ||
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_182700 | SP8 | 3484 | 3502 | U | A | A | U | U | G | C | U | C | A | U | u | G | u | A | A | U | G | U | 46 | 2 | 11 | false | <90% | 3670 | |||
| NM_198956 | SP8 | 3580 | 3598 | U | A | A | U | U | G | C | U | C | A | U | u | G | u | A | A | U | G | U | 46 | 2 | 11 | false | <90% | 3766 | |||
| NM_172344 | KCNG3 | 2290 | 2308 | U | A | A | U | U | u | C | U | C | A | U | A | u | C | A | A | U | G | U | 26 | 2 | 6 | false | <90% | 3791 | |||
| NM_133329 | KCNG3 | 2323 | 2341 | U | A | A | U | U | u | C | U | C | A | U | A | u | C | A | A | U | G | U | 26 | 2 | 6 | false | <90% | 3824 | |||
| NM_138316 | PANK1 | 1729 | 1747 | U | A | A | U | U | G | u | U | C | A | U | A | u | C | A | A | U | G | a | 18 | 3 | 6 | false | <90% | 2525 | |||
| NM_148978 | PANK1 | 1906 | 1924 | U | A | A | U | U | G | u | U | C | A | U | A | u | C | A | A | U | G | a | 18 | 3 | 6 | false | <90% | 2702 | |||
| NM_148977 | PANK1 | 2571 | 2589 | U | A | A | U | U | G | u | U | C | A | U | A | u | C | A | A | U | G | a | 18 | 3 | 6 | false | <90% | 3367 | |||
3 prime UTR Seed matches
Hits to same gene : 0
Hits to other genes : 1687
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