Automatic recommendation
Not OK - siRNA is not specific
14 hits were found for UAGAGAGAAUGGUGCUCUC (10 guide strand hits and 4 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 | |||||||||||||
| XR_019244 | LOC389120 | 573 | 591 | a | g | G | A | G | A | G | A | A | U | G | G | U | G | C | U | C | c | C | 83 | 3 | 15 | ac | false | <90% | 3571 | ||
| XR_017199 | LOC389120 | 573 | 591 | a | g | G | A | G | A | G | A | A | U | G | G | U | G | C | U | C | c | C | 83 | 3 | 15 | ac | false | <90% | 3571 | ||
| NM_152888 | COL22A1 | 1227 | 1245 | g | A | G | A | G | A | G | A | A | U | G | G | a | G | C | U | C | a | g | 79 | 4 | 11 | false | <90% | 6366 | |||
| NM_014790 | JAKMIP2 | 2694 | 2712 | a | g | G | A | G | A | G | A | A | U | G | G | a | G | C | U | C | U | u | 71 | 4 | 10 | false | <90% | 3357 | |||
| NM_015678 | NBEA | 3455 | 3473 | U | g | G | A | G | A | G | A | A | U | G | G | U | G | C | c | C | U | u | 57 | 3 | 13 | c | false | <90% | 10812 | ||
| NM_020375 | C12orf5 | 2069 | 2087 | g | g | G | A | G | A | G | A | A | U | G | u | U | G | C | U | C | U | g | 47 | 4 | 9 | false | <90% | 8237 | |||
| NM_001046 | SLC12A2 | 6520 | 6538 | U | A | G | A | G | A | G | A | A | U | G | G | U | G | g | U | g | U | u | 46 | 3 | 14 | c | false | <90% | 6891 | ||
| NM_000960 | PTGIR | 1478 | 1496 | c | A | G | A | a | A | G | A | A | U | G | G | U | u | C | U | C | U | C | 27 | 3 | 8 | c | false | <90% | 2103 | ||
| NM_145257 | C1orf96 | 2254 | 2272 | a | A | G | A | G | A | u | A | A | U | G | G | U | G | C | U | C | U | g | 26 | 3 | 11 | bc | false | <90% | 5174 | ||
| NM_176810 | NLRP13 | 2631 | 2649 | U | A | G | A | G | A | G | A | c | U | G | G | a | G | C | U | C | U | g | 24 | 3 | 8 | false | <90% | 3157 | |||
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_033208 | TIGD7 | 211 | 229 | u | u | G | A | G | C | A | C | C | A | U | U | C | U | C | U | u | U | u | 58 | 4 | 14 | ac | false | <90% | 2569 | ||
| XM_933711 | LOC646570 | 1077 | 1095 | a | A | G | A | G | C | A | C | C | A | c | U | C | U | C | U | C | c | A | 34 | 3 | 9 | c | false | <90% | 1218 | ||
| XM_944905 | LOC651752 | 1077 | 1095 | a | A | G | A | G | C | A | C | C | A | c | U | C | U | C | U | C | c | A | 34 | 3 | 9 | c | false | <90% | 1218 | ||
| NM_015289 | VPS39 | 3525 | 3543 | G | A | G | A | G | C | A | u | C | A | U | U | C | U | C | U | g | c | c | 6 | 4 | 8 | c | false | <90% | 4851 | ||
3 prime UTR Seed matches
Hits to same gene : 0
Hits to other genes : 1693
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