Automatic recommendation
Not OK - siRNA is not specific
15 hits were found for GAGAAACAACCUAGUGAUG (13 guide strand hits and 2 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_024949 | WWC2 | 1805 | 1823 | G | u | G | A | A | A | C | A | A | C | C | U | A | G | U | G | A | a | a | 80 | 3 | 15 | ac | false | <90% | 6492 | ||
| NM_022725 | FANCF | 2799 | 2817 | a | A | G | A | A | A | C | A | A | C | C | c | A | G | U | G | A | a | G | 61 | 3 | 10 | false | <90% | 3309 | |||
| NM_032949 | PCDH8 | 3547 | 3565 | c | u | G | A | A | A | C | A | A | C | C | U | A | G | U | G | u | U | u | 58 | 4 | 14 | ac | false | <90% | 3785 | ||
| NM_002590 | PCDH8 | 3838 | 3856 | c | u | G | A | A | A | C | A | A | C | C | U | A | G | U | G | u | U | u | 58 | 4 | 14 | ac | false | <90% | 4076 | ||
| NM_020792 | AADACL1 | 2277 | 2295 | a | u | G | A | A | A | C | A | A | C | C | U | A | G | U | G | u | U | u | 58 | 4 | 14 | ac | false | <90% | 4289 | ||
| NM_001083625 | ANKRD12 | 3645 | 3663 | G | A | G | A | A | A | C | A | A | C | C | U | A | a | a | G | A | U | G | 55 | 2 | 13 | c | false | <90% | 10459 | ||
| NM_015208 | ANKRD12 | 3714 | 3732 | G | A | G | A | A | A | C | A | A | C | C | U | A | a | a | G | A | U | G | 55 | 2 | 13 | c | false | <90% | 10528 | ||
| NM_177966 | 2'-PDE | 3148 | 3166 | G | A | G | A | A | A | C | u | A | C | C | U | A | c | U | G | A | U | a | 13 | 3 | 7 | c | false | <90% | 3923 | ||
| NM_014805 | EPM2AIP1 | 3981 | 3999 | G | A | G | A | A | A | C | A | A | C | a | U | A | G | U | G | g | a | a | 7 | 4 | 10 | c | false | <90% | 5567 | ||
| NM_178123 | SESTD1 | 1113 | 1131 | c | A | G | c | A | A | C | A | A | C | u | U | A | G | U | G | A | U | G | 0 | 3 | 8 | c | false | <90% | 3234 | ||
| NM_000749 | CHRNB3 | 1260 | 1278 | c | A | G | A | A | A | C | A | g | C | u | U | A | G | U | G | A | U | G | -23 | 3 | 8 | c | false | <90% | 1953 | ||
| XM_001133506 | LOC729534 | 657 | 675 | G | A | G | A | A | A | g | c | A | C | C | U | A | G | U | G | A | U | u | -33 | 3 | 10 | bc | false | <90% | 878 | ||
| XM_001133339 | LOC731569 | 657 | 675 | G | A | G | A | A | A | g | c | A | C | C | U | A | G | U | G | A | U | u | -33 | 3 | 10 | bc | false | <90% | 878 | ||
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_020689 | SLC24A3 | 2955 | 2973 | u | c | U | C | A | C | U | A | G | G | U | U | c | U | U | U | C | U | a | 71 | 4 | 10 | false | <90% | 3905 | |||
| NM_015944 | AMDHD2 | 387 | 405 | u | A | U | C | A | C | a | A | G | G | U | U | G | U | U | c | C | U | C | 5 | 3 | 8 | c | false | <90% | 1540 | ||
3 prime UTR Seed matches
Hits to same gene : 0
Hits to other genes : 2641
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