Automatic recommendation
OK - siRNA is specific for both sense and antisense (guide) strands
18 hits were found for AACUACUAUGACAGCUUCA (17 guide strand hits and 1 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_001642 | APLP2 | 889 | 907 | u | A | C | U | A | C | U | A | U | G | A | C | A | c | C | U | U | C | A | 78 | 2 | 12 | c | false | <90% | 3727 | ||
| NM_004504 | HRB | 2551 | 2569 | A | A | C | U | A | C | U | A | U | G | A | C | u | G | C | U | a | C | A | 66 | 2 | 12 | false | <90% | 4878 | |||
| NM_001013841 | STAP2 | 155 | 173 | c | A | C | U | A | C | U | A | U | G | A | g | A | G | C | U | U | u | c | 56 | 4 | 10 | false | <90% | 1419 | |||
| NM_017720 | STAP2 | 155 | 173 | c | A | C | U | A | C | U | A | U | G | A | g | A | G | C | U | U | u | c | 56 | 4 | 10 | false | <90% | 1557 | |||
| NM_013305 | ST8SIA5 | 1574 | 1592 | c | A | C | U | A | C | U | A | U | G | A | C | A | a | C | g | U | C | A | 52 | 3 | 12 | c | false | <90% | 2627 | ||
| NM_182648 | BAZ1A | 4865 | 4883 | g | A | C | U | A | C | U | A | U | G | A | C | A | u | C | a | U | C | A | 52 | 3 | 12 | c | false | <90% | 5935 | ||
| NM_013448 | BAZ1A | 4961 | 4979 | g | A | C | U | A | C | U | A | U | G | A | C | A | u | C | a | U | C | A | 52 | 3 | 12 | c | false | <90% | 6031 | ||
| NM_012320 | LYPLA3 | 1107 | 1125 | u | u | C | U | A | C | U | A | U | G | A | g | A | G | C | U | U | C | c | 47 | 4 | 9 | false | <90% | 2764 | |||
| NM_138328 | RHBDL3 | 468 | 486 | u | g | g | U | A | C | U | A | U | G | A | C | A | G | C | U | a | C | A | 43 | 4 | 13 | c | false | <90% | 4688 | ||
| XM_929841 | LOC646879 | 465 | 483 | A | u | C | U | u | C | U | A | U | G | A | C | A | G | C | U | U | C | u | 32 | 3 | 13 | bc | false | <90% | 504 | ||
| XM_941137 | LOC646879 | 465 | 483 | A | u | C | U | u | C | U | A | U | G | A | C | A | G | C | U | U | C | u | 32 | 3 | 13 | bc | false | <90% | 504 | ||
| NM_005238 | ETS1 | 1113 | 1131 | c | c | C | U | c | C | U | A | U | G | A | C | A | G | C | U | U | C | g | 30 | 4 | 13 | bc | false | <90% | 5228 | ||
| NM_013945 | PAX7 | 1671 | 1689 | A | g | C | U | A | C | U | c | U | G | A | C | A | G | C | U | U | C | A | 26 | 2 | 11 | bc | false | <90% | 2255 | ||
| NM_002584 | PAX7 | 1677 | 1695 | A | g | C | U | A | C | U | c | U | G | A | C | A | G | C | U | U | C | A | 26 | 2 | 11 | bc | false | <90% | 2272 | ||
| NM_006011 | ST8SIA2 | 1143 | 1161 | c | A | C | U | A | u | U | A | U | G | A | C | A | G | C | c | U | C | A | 8 | 3 | 9 | c | false | <90% | 5626 | ||
| NM_015167 | JMJD6 | 412 | 430 | A | A | C | U | A | C | U | A | c | G | A | g | A | G | C | U | U | C | u | 1 | 3 | 8 | false | <90% | 1834 | |||
| NM_001081461 | JMJD6 | 412 | 430 | A | A | C | U | A | C | U | A | c | G | A | g | A | G | C | U | U | C | u | 1 | 3 | 8 | false | <90% | 5445 | |||
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_004849 | ATG5 | 1936 | 1954 | a | G | A | A | G | C | U | G | U | C | A | U | A | G | a | A | u | U | U | 49 | 3 | 13 | c | false | <90% | 3244 | ||
3 prime UTR Seed matches
Hits to same gene : 0
Hits to other genes : 1692
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