Automatic recommendation
OK - siRNA is specific for both sense and antisense (guide) strands
21 hits were found for AUUACUACAGACACUGGUA (13 guide strand hits and 8 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_003108 | SOX11 | 5957 | 5975 | A | U | g | A | C | U | A | C | A | G | A | C | A | C | U | G | G | g | c | 72 | 3 | 14 | c | false | <90% | 8737 | ||
| NM_152781 | C17orf66 | 941 | 959 | u | g | U | A | C | U | A | C | A | G | A | C | A | C | U | G | a | U | c | 58 | 4 | 14 | ac | false | <90% | 1969 | ||
| NM_007069 | HRASLS3 | 462 | 480 | c | U | U | u | C | U | A | C | A | G | A | C | A | C | U | G | G | g | c | 53 | 4 | 13 | c | false | <90% | 1067 | ||
| XR_019366 | LOC401959 | 174 | 192 | u | c | U | A | a | U | A | C | A | G | A | C | A | C | U | G | G | U | A | 35 | 3 | 14 | bc | false | <90% | 861 | ||
| XR_017431 | LOC401959 | 174 | 192 | u | c | U | A | a | U | A | C | A | G | A | C | A | C | U | G | G | U | A | 35 | 3 | 14 | bc | false | <90% | 861 | ||
| NM_003375 | VDAC2 | 331 | 349 | u | c | U | A | a | U | A | C | A | G | A | C | A | C | U | G | G | U | A | 35 | 3 | 14 | bc | false | <90% | 1522 | ||
| XM_001133585 | LOC729317 | 309 | 327 | u | c | U | A | a | U | A | C | A | G | A | C | A | C | U | G | G | U | A | 35 | 3 | 14 | bc | false | <90% | 1706 | ||
| XM_941786 | LOC647153 | 314 | 332 | u | c | U | A | a | U | A | C | A | G | A | C | A | C | U | G | G | U | A | 35 | 3 | 14 | bc | false | <90% | 1711 | ||
| NM_006951 | TAF5 | 2277 | 2295 | u | U | U | A | C | U | A | C | A | G | c | C | A | C | U | G | G | g | c | 29 | 4 | 9 | c | false | <90% | 3283 | ||
| NM_004857 | AKAP5 | 2309 | 2327 | A | U | U | A | u | U | A | C | A | G | A | C | A | C | U | G | a | a | A | 22 | 3 | 11 | c | false | <90% | 2601 | ||
| NR_002826 | LOC401010 | 1847 | 1865 | u | g | U | A | C | U | A | C | A | G | c | C | A | C | U | G | G | U | g | 20 | 4 | 8 | c | false | <90% | 2738 | ||
| NM_006918 | SC5DL | 6421 | 6439 | A | U | U | A | a | g | A | C | A | G | A | C | A | C | U | G | G | U | g | -19 | 3 | 12 | bc | false | <90% | 6946 | ||
| NM_001024956 | SC5DL | 6494 | 6512 | A | U | U | A | a | g | A | C | A | G | A | C | A | C | U | G | G | U | g | -19 | 3 | 12 | bc | false | <90% | 7019 | ||
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 | |||||||||||||
| XM_939772 | HMFN0672 | 523 | 541 | U | A | C | C | A | G | U | G | U | C | U | G | g | A | G | a | A | A | g | 58 | 3 | 12 | false | <90% | 2633 | |||
| XM_372035 | HMFN0672 | 523 | 541 | U | A | C | C | A | G | U | G | U | C | U | G | g | A | G | a | A | A | g | 58 | 3 | 12 | false | <90% | 2633 | |||
| NM_022481 | CENTD3 | 1721 | 1739 | c | A | C | g | A | G | U | G | U | C | U | G | g | A | G | U | A | A | U | 50 | 3 | 8 | false | <90% | 5281 | |||
| XM_497354 | FLJ30092 | 6654 | 6672 | U | A | a | C | c | G | U | G | U | C | U | G | U | A | G | U | A | A | a | 23 | 3 | 13 | bc | false | <90% | 11209 | ||
| XM_942665 | FLJ30092 | 6654 | 6672 | U | A | a | C | c | G | U | G | U | C | U | G | U | A | G | U | A | A | a | 23 | 3 | 13 | bc | false | <90% | 11209 | ||
| NM_012286 | MORF4L2 | 1364 | 1382 | U | A | C | C | A | G | U | G | U | a | U | G | c | A | G | U | A | A | U | 6 | 2 | 9 | false | <90% | 1826 | |||
| NM_004171 | SLC1A2 | 6662 | 6680 | U | c | u | C | A | G | U | a | U | C | U | G | U | A | G | U | A | A | U | 6 | 3 | 11 | bc | false | <90% | 12021 | ||
| NM_024690 | MUC16 | 4450 | 4468 | g | A | C | C | u | G | U | c | U | C | U | G | U | A | G | U | A | A | U | -15 | 3 | 11 | bc | false | <90% | 43816 | ||
3 prime UTR Seed matches
Hits to same gene : 0
Hits to other genes : 1646
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