Automatic recommendation
OK - siRNA is specific for both sense and antisense (guide) strands
10 hits were found for GAAACUUGGCAUGACAGCU (4 guide strand hits and 6 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_145909 | ZNF323 | 138 | 156 | G | A | c | A | C | U | U | G | G | C | A | U | G | A | C | A | G | u | g | 72 | 3 | 14 | c | false | <90% | 3176 | ||
| NM_173517 | VKORC1L1 | 399 | 417 | a | u | u | A | C | U | U | G | G | C | A | U | G | A | C | A | G | C | a | 62 | 4 | 15 | bc | false | <90% | 1148 | ||
| XM_001126195 | LOC727942 | 5620 | 5638 | G | A | A | A | C | U | U | G | G | C | A | U | u | A | C | A | u | u | a | 58 | 4 | 12 | false | <90% | 5773 | |||
| NM_020829 | KIAA1432 | 1803 | 1821 | u | A | A | A | C | c | U | G | G | C | A | g | G | A | C | A | G | C | U | 0 | 3 | 7 | false | <90% | 4125 | |||
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_025063 | C1orf129 | 349 | 367 | A | G | u | U | G | U | C | A | U | G | C | C | A | A | G | U | c | U | u | 51 | 3 | 13 | c | false | <90% | 2258 | ||
| NM_152133 | TAGAP | 2733 | 2751 | A | a | a | U | G | U | C | A | U | G | C | C | A | A | u | U | U | U | C | 44 | 3 | 11 | c | false | <90% | 3196 | ||
| NM_054114 | TAGAP | 2900 | 2918 | A | a | a | U | G | U | C | A | U | G | C | C | A | A | u | U | U | U | C | 44 | 3 | 11 | c | false | <90% | 3363 | ||
| NM_003566 | EEA1 | 4729 | 4747 | A | G | C | U | u | U | C | A | U | G | C | C | A | A | G | U | U | U | a | 43 | 2 | 13 | bc | false | <90% | 8019 | ||
| NM_173178 | IL1F8 | 835 | 853 | A | G | C | U | G | c | C | A | U | G | C | C | c | A | G | U | U | U | a | 21 | 3 | 6 | false | <90% | 922 | |||
| NM_018696 | ELAC1 | 1904 | 1922 | A | G | C | U | G | U | C | c | U | G | C | a | A | A | G | U | U | U | u | 0 | 3 | 7 | false | <90% | 2233 | |||
3 prime UTR Seed matches
Hits to same gene : 0
Hits to other genes : 2989
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