Automatic recommendation
OK - siRNA is specific for both sense and antisense (guide) strands
15 hits were found for GCAGCACUAGUAGAGACAA (2 guide strand hits and 13 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_001013732 | LOC442213 | 827 | 845 | c | C | A | G | g | A | C | U | A | G | c | A | G | A | G | A | C | A | A | -14 | 3 | 8 | c | false | <90% | 1533 | ||
| NM_020463 | SMEK2 | 3299 | 3317 | u | C | A | G | C | A | C | U | u | u | U | A | G | A | G | A | C | A | A | -44 | 3 | 9 | bc | false | <90% | 4172 | ||
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_006475 | POSTN | 34 | 52 | U | U | u | U | C | U | C | U | A | C | U | A | u | U | G | C | U | G | C | 70 | 2 | 9 | false | <90% | 3213 | |||
| XR_015966 | LOC729403 | 623 | 641 | c | U | G | U | C | U | C | U | A | C | U | g | G | c | G | C | U | G | C | 44 | 3 | 10 | false | <90% | 1005 | |||
| XR_015948 | LOC731612 | 623 | 641 | c | U | G | U | C | U | C | U | A | C | U | g | G | c | G | C | U | G | C | 44 | 3 | 10 | false | <90% | 1005 | |||
| XR_019011 | LOC651042 | 1575 | 1593 | U | U | a | U | C | U | C | U | A | C | U | g | G | U | G | C | U | G | g | 41 | 3 | 8 | false | <90% | 1853 | |||
| NM_004232 | SOCS6 | 5097 | 5115 | a | U | G | U | C | U | C | U | g | C | U | A | G | U | G | C | U | a | C | 35 | 3 | 8 | c | false | <90% | 5846 | ||
| NM_006784 | WDR3 | 2515 | 2533 | g | a | a | U | C | U | C | U | A | C | U | u | G | U | G | C | U | G | C | 33 | 4 | 8 | false | <90% | 3850 | |||
| XR_016109 | LOC642259 | 642 | 660 | c | U | G | c | C | U | C | U | A | C | U | g | G | U | G | C | U | G | C | 27 | 3 | 7 | false | <90% | 1045 | |||
| XR_018113 | LOC642203 | 642 | 660 | c | U | G | c | C | U | C | U | A | C | U | g | G | U | G | C | U | G | C | 27 | 3 | 7 | false | <90% | 1045 | |||
| XR_017396 | LOC647001 | 600 | 618 | c | U | G | c | C | U | C | U | A | C | U | g | G | U | G | C | U | G | C | 27 | 3 | 7 | false | <90% | 1067 | |||
| XR_018331 | LOC648495 | 601 | 619 | c | U | G | c | C | U | C | U | A | C | U | g | G | U | G | C | U | G | C | 27 | 3 | 7 | false | <90% | 1068 | |||
| NM_022367 | SEMA4A | 2056 | 2074 | g | g | G | U | C | U | C | U | A | C | c | A | G | U | G | C | U | G | g | 20 | 4 | 8 | c | false | <90% | 3257 | ||
| XR_018352 | LOC441893 | 606 | 624 | a | U | G | U | g | U | C | U | A | C | U | g | G | U | G | C | U | G | C | 12 | 3 | 7 | false | <90% | 988 | |||
| XR_017298 | LOC441893 | 606 | 624 | a | U | G | U | g | U | C | U | A | C | U | g | G | U | G | C | U | G | C | 12 | 3 | 7 | false | <90% | 988 | |||
3 prime UTR Seed matches
Hits to same gene : 0
Hits to other genes : 1861
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