Automatic recommendation
OK - siRNA is specific for both sense and antisense (guide) strands
12 hits were found for UUAUGGCAAUGGAGUCAUA (8 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 | |||||||||||||
| NM_012096 | APPL1 | 4802 | 4820 | c | U | A | U | G | G | C | A | A | U | G | a | A | G | U | C | A | g | u | 56 | 4 | 10 | false | <90% | 6061 | |||
| NM_177972 | TUB | 1178 | 1196 | U | U | A | U | G | a | C | A | A | U | G | G | A | G | U | C | A | a | c | 29 | 3 | 11 | c | false | <90% | 6172 | ||
| NM_003320 | TUB | 1435 | 1453 | U | U | A | U | G | a | C | A | A | U | G | G | A | G | U | C | A | a | c | 29 | 3 | 11 | c | false | <90% | 6429 | ||
| NM_024334 | TMEM43 | 664 | 682 | c | c | A | U | G | G | C | A | g | U | G | G | A | G | U | C | A | U | u | 21 | 4 | 9 | bc | false | <90% | 3254 | ||
| NM_181616 | KRTAP20-2 | 36 | 54 | U | U | A | U | G | G | C | u | A | U | G | G | A | G | U | C | c | U | g | 9 | 3 | 8 | c | false | <90% | 198 | ||
| NM_032199 | ARID5B | 6433 | 6451 | a | a | u | U | G | G | C | A | g | U | G | G | A | G | U | C | A | U | A | 6 | 4 | 10 | bc | false | <90% | 7507 | ||
| NM_001035 | RYR2 | 12231 | 12249 | c | g | A | U | G | G | C | A | A | g | G | G | A | G | U | C | A | U | u | -1 | 4 | 8 | bc | false | <90% | 16365 | ||
| NM_001389 | DSCAM | 2558 | 2576 | U | U | A | U | G | G | C | A | A | a | G | c | A | G | U | C | A | U | c | -21 | 3 | 9 | false | <90% | 7110 | |||
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_001343 | DAB2 | 1419 | 1437 | c | A | U | G | A | C | U | C | C | A | U | a | G | C | C | A | U | u | A | 61 | 3 | 10 | false | <90% | 3268 | |||
| XM_001128282 | LOC728138 | 40 | 58 | a | A | U | G | A | C | U | C | C | A | a | U | G | C | C | A | U | A | g | 31 | 3 | 9 | c | false | <90% | 2619 | ||
| NM_138335 | GNPDA2 | 1314 | 1332 | U | A | U | G | A | C | U | C | C | A | g | U | G | g | C | A | U | A | u | 14 | 3 | 10 | c | false | <90% | 1939 | ||
| NM_016021 | UBE2J1 | 3003 | 3021 | U | A | U | a | A | C | U | C | u | A | U | U | G | C | C | A | U | A | A | 3 | 2 | 10 | bc | false | <90% | 4360 | ||
3 prime UTR Seed matches
Hits to same gene : 0
Hits to other genes : 1334
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