Automatic recommendation
OK - siRNA is specific for both sense and antisense (guide) strands
14 hits were found for GACUAGUAGAGACAAGAUA (7 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_130807 | MOBKL2A | 2085 | 2103 | u | u | u | U | A | G | U | A | G | A | G | A | C | A | A | G | A | U | u | 62 | 4 | 15 | bc | false | <90% | 3347 | ||
| NM_022476 | AKTIP | 1735 | 1753 | G | u | u | U | A | G | U | A | G | A | G | A | C | A | A | a | A | U | A | 42 | 3 | 12 | c | false | <90% | 2193 | ||
| NM_001012398 | AKTIP | 1764 | 1782 | G | u | u | U | A | G | U | A | G | A | G | A | C | A | A | a | A | U | A | 42 | 3 | 12 | c | false | <90% | 2222 | ||
| NM_001013732 | LOC442213 | 831 | 849 | G | A | C | U | A | G | c | A | G | A | G | A | C | A | A | G | c | a | g | 2 | 4 | 9 | c | false | <90% | 1533 | ||
| XM_376679 | FLJ25778 | 5300 | 5318 | G | A | C | U | g | G | U | A | G | u | G | A | C | A | A | G | A | U | u | -39 | 3 | 8 | bc | false | <90% | 8672 | ||
| XM_379933 | FLJ25778 | 5300 | 5318 | G | A | C | U | g | G | U | A | G | u | G | A | C | A | A | G | A | U | u | -39 | 3 | 8 | bc | false | <90% | 8672 | ||
| XM_939098 | FLJ25778 | 5300 | 5318 | G | A | C | U | g | G | U | A | G | u | G | A | C | A | A | G | A | U | u | -39 | 3 | 8 | bc | false | <90% | 8672 | ||
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_016451 | COPB1 | 1337 | 1355 | g | A | U | C | U | U | G | U | C | U | C | U | u | C | U | A | G | a | a | 79 | 4 | 11 | false | <90% | 3528 | |||
| NM_024596 | MCPH1 | 5775 | 5793 | a | A | c | C | U | U | G | U | C | U | C | U | A | C | U | A | G | a | a | 70 | 4 | 14 | c | false | <90% | 8032 | ||
| NM_018137 | PRMT6 | 1812 | 1830 | a | u | U | C | U | U | G | U | C | U | C | U | A | C | U | A | u | U | a | 58 | 4 | 14 | ac | false | <90% | 2506 | ||
| NM_033141 | MAP3K9 | 5417 | 5435 | U | A | U | C | c | U | G | U | C | U | C | U | A | C | U | A | a | a | a | 17 | 4 | 11 | c | false | <90% | 5602 | ||
| NM_001077484 | SLC38A1 | 1418 | 1436 | U | A | U | C | U | U | G | g | C | U | a | U | A | C | U | A | G | U | g | -28 | 3 | 7 | c | false | <90% | 8148 | ||
| NM_030674 | SLC38A1 | 1757 | 1775 | U | A | U | C | U | U | G | g | C | U | a | U | A | C | U | A | G | U | g | -28 | 3 | 7 | c | false | <90% | 8487 | ||
| NM_144689 | ZNF420 | 2547 | 2565 | U | A | U | C | U | U | a | g | C | U | C | U | A | C | U | A | G | U | u | -33 | 3 | 10 | bc | false | <90% | 2990 | ||
3 prime UTR Seed matches
Hits to same gene : 0
Hits to other genes : 703
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