Automatic recommendation
OK - siRNA is specific for both sense and antisense (guide) strands
28 hits were found for GAAGAAUGUCAAAGGAUGA (19 guide strand hits and 9 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_005596 | NFIB | 575 | 593 | a | g | c | G | A | A | U | G | U | C | A | A | A | G | G | A | U | G | A | 67 | 3 | 16 | bc | false | <90% | 8159 | ||
| NM_001007100 | SCP2 | 296 | 314 | G | A | A | G | A | A | U | G | g | C | A | A | A | G | G | A | U | c | A | 37 | 2 | 8 | c | false | <90% | 1438 | ||
| NM_001007099 | SCP2 | 305 | 323 | G | A | A | G | A | A | U | G | g | C | A | A | A | G | G | A | U | c | A | 37 | 2 | 8 | c | false | <90% | 1447 | ||
| NM_002979 | SCP2 | 1555 | 1573 | G | A | A | G | A | A | U | G | g | C | A | A | A | G | G | A | U | c | A | 37 | 2 | 8 | c | false | <90% | 2697 | ||
| NM_014390 | SND1 | 1687 | 1705 | u | A | A | G | A | A | U | G | g | C | A | A | A | G | G | A | U | u | g | 30 | 4 | 8 | c | false | <90% | 3522 | ||
| NM_020813 | ZNF471 | 209 | 227 | G | A | A | G | A | A | U | G | g | C | A | A | u | G | G | A | U | G | A | 29 | 2 | 8 | false | <90% | 4985 | |||
| NM_004807 | HS6ST1 | 1416 | 1434 | c | A | A | G | A | c | U | G | U | C | A | A | g | G | G | A | U | G | A | 24 | 3 | 6 | false | <90% | 2051 | |||
| XM_001132928 | LOC728969 | 1423 | 1441 | c | A | A | G | A | c | U | G | U | C | A | A | g | G | G | A | U | G | A | 24 | 3 | 6 | false | <90% | 4055 | |||
| NM_003478 | CUL5 | 4868 | 4886 | c | A | A | G | A | A | U | G | c | C | A | A | A | G | G | A | g | G | A | 14 | 3 | 7 | c | false | <90% | 6408 | ||
| NM_002547 | OPHN1 | 5497 | 5515 | u | A | A | G | A | A | U | G | c | C | A | A | A | G | a | A | U | G | A | 13 | 3 | 7 | c | false | <90% | 7350 | ||
| NM_153442 | GPR26 | 7485 | 7503 | G | A | A | G | A | A | U | G | g | C | A | A | A | G | G | A | a | G | g | 11 | 3 | 8 | c | false | <90% | 7512 | ||
| NM_145027 | KIF6 | 1644 | 1662 | G | A | A | G | A | A | g | G | U | C | A | A | A | G | a | A | U | G | c | 4 | 3 | 7 | c | false | <90% | 2917 | ||
| NM_003292 | TPR | 3701 | 3719 | a | g | A | G | A | A | U | G | U | u | A | A | A | G | G | A | U | G | A | 3 | 3 | 9 | bc | false | <90% | 9727 | ||
| XM_937141 | LOC347364 | 146 | 164 | a | A | A | G | A | A | a | G | U | C | A | g | A | G | G | A | U | G | A | -2 | 3 | 7 | false | <90% | 282 | |||
| XM_926024 | LOC347364 | 146 | 164 | a | A | A | G | A | A | a | G | U | C | A | g | A | G | G | A | U | G | A | -2 | 3 | 7 | false | <90% | 282 | |||
| NM_016312 | WBP11 | 1951 | 1969 | a | A | A | G | A | A | a | G | U | C | A | g | A | G | G | A | U | G | A | -2 | 3 | 7 | false | <90% | 2690 | |||
| NM_017881 | C9orf95 | 577 | 595 | G | A | A | G | A | A | U | G | U | a | A | A | A | G | G | A | g | G | A | -6 | 2 | 9 | c | false | <90% | 1172 | ||
| NM_014568 | GALNT5 | 1151 | 1169 | G | A | A | G | u | u | U | G | U | C | A | A | A | G | G | A | U | G | A | -14 | 2 | 13 | bc | false | <90% | 3131 | ||
| NM_003777 | DNAH11 | 12911 | 12929 | c | A | A | G | A | A | U | G | U | g | A | g | A | G | G | A | U | G | A | -18 | 3 | 8 | false | <90% | 14188 | |||
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_001371 | DNAH8 | 8893 | 8911 | c | C | A | U | C | C | U | U | U | G | A | C | u | U | U | C | U | g | g | 79 | 4 | 11 | false | <90% | 14472 | |||
| NM_015553 | PIP3-E | 5306 | 5324 | U | g | g | U | C | C | U | U | U | G | A | C | c | U | U | C | U | U | C | 58 | 3 | 9 | false | <90% | 6687 | |||
| XM_001133349 | NOTCH2 | 7519 | 7537 | U | C | c | U | C | C | U | U | g | G | A | C | A | U | U | C | U | U | u | 15 | 3 | 9 | bc | false | <90% | 10836 | ||
| NM_024408 | NOTCH2 | 8108 | 8126 | U | C | c | U | C | C | U | U | g | G | A | C | A | U | U | C | U | U | u | 15 | 3 | 9 | bc | false | <90% | 11433 | ||
| NM_001080479 | RGNEF | 2319 | 2337 | c | C | A | U | C | C | U | U | g | G | A | a | A | U | U | C | U | U | C | 4 | 3 | 7 | false | <90% | 5252 | |||
| XM_937885 | RGNEF | 2319 | 2337 | c | C | A | U | C | C | U | U | g | G | A | a | A | U | U | C | U | U | C | 4 | 3 | 7 | false | <90% | 5252 | |||
| XM_932949 | RGNEF | 2319 | 2337 | c | C | A | U | C | C | U | U | g | G | A | a | A | U | U | C | U | U | C | 4 | 3 | 7 | false | <90% | 6574 | |||
| NM_003747 | TNKS | 8430 | 8448 | U | C | c | U | C | C | U | U | U | c | A | C | A | U | U | C | U | U | u | -7 | 3 | 8 | bc | false | <90% | 9599 | ||
| NM_014294 | TRAM1 | 2434 | 2452 | U | C | A | U | C | C | U | U | U | a | A | g | A | U | U | C | U | U | a | -21 | 3 | 9 | false | <90% | 2805 | |||
3 prime UTR Seed matches
Hits to same gene : 0
Hits to other genes : 2959
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