Automatic recommendation
OK - siRNA is specific for both sense and antisense (guide) strands
12 hits were found for UUCAGCGAACAAGAGGCGC (11 guide strand hits and 1 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_015310 | PSD3 | 1343 | 1361 | a | U | C | A | G | C | G | A | A | C | A | A | G | A | G | G | a | G | C | 74 | 2 | 15 | ac | false | <90% | 11687 | ||
| NM_203316 | DPAGT1 | 171 | 189 | U | U | C | A | G | C | G | A | A | C | A | A | G | A | u | c | C | G | g | 44 | 3 | 14 | c | false | <90% | 2038 | ||
| NM_001382 | DPAGT1 | 171 | 189 | U | U | C | A | G | C | G | A | A | C | A | A | G | A | u | c | C | G | g | 44 | 3 | 14 | c | false | <90% | 2159 | ||
| XM_001133434 | LOC732422 | 180 | 198 | g | g | C | A | G | C | G | A | A | C | g | A | G | A | G | G | C | G | g | 20 | 4 | 8 | c | false | <90% | 537 | ||
| NM_001040069 | LOC649159 | 314 | 332 | g | g | C | A | G | C | G | A | A | C | c | A | G | A | G | G | C | G | g | 20 | 4 | 8 | c | false | <90% | 1452 | ||
| XM_001130436 | LOC731687 | 2059 | 2077 | c | U | g | A | G | g | G | A | A | C | A | A | G | A | G | G | C | G | C | 15 | 3 | 13 | bc | false | <90% | 2537 | ||
| XM_001132573 | LOC730131 | 2061 | 2079 | c | U | g | A | G | g | G | A | A | C | A | A | G | A | G | G | C | G | C | 15 | 3 | 13 | bc | false | <90% | 2539 | ||
| NM_005863 | NET1 | 262 | 280 | U | U | C | A | G | a | G | A | A | C | A | A | G | A | G | G | a | G | C | 13 | 2 | 10 | c | false | <90% | 3297 | ||
| NM_001013690 | LOC401720 | 1479 | 1497 | a | U | C | A | G | C | G | A | g | C | u | A | G | A | G | G | C | G | C | -23 | 3 | 8 | c | false | <90% | 4533 | ||
| XM_937860 | USP27X | 1302 | 1320 | U | U | C | A | G | C | G | A | A | a | c | A | G | A | G | G | C | G | C | -44 | 2 | 9 | c | false | <90% | 1674 | ||
| XM_372213 | USP27X | 1302 | 1320 | U | U | C | A | G | C | G | A | A | a | c | A | G | A | G | G | C | G | C | -44 | 2 | 9 | c | false | <90% | 1674 | ||
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_207662 | ZC3H14 | 409 | 427 | G | C | u | C | C | U | C | U | U | G | U | U | C | a | C | U | G | A | A | 60 | 2 | 10 | c | false | <90% | 3018 | ||
3 prime UTR Seed matches
Hits to same gene : 0
Hits to other genes : 432
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