Automatic recommendation
OK - siRNA is specific for both sense and antisense (guide) strands
12 hits were found for UGCCCGUUUUCAAACCGGG (7 guide strand hits and 5 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_019224 | LOC649574 | 419 | 437 | U | G | C | C | a | G | U | U | U | U | C | A | A | A | C | C | G | G | c | 43 | 2 | 13 | bc | false | <90% | 2147 | ||
| NM_152795 | HIF3A | 3303 | 3321 | U | G | C | C | u | G | U | U | U | U | C | A | A | A | C | C | u | u | a | 17 | 4 | 11 | c | false | <90% | 5850 | ||
| NM_152794 | HIF3A | 3317 | 3335 | U | G | C | C | u | G | U | U | U | U | C | A | A | A | C | C | u | u | a | 17 | 4 | 11 | c | false | <90% | 5864 | ||
| NM_022462 | HIF3A | 3361 | 3379 | U | G | C | C | u | G | U | U | U | U | C | A | A | A | C | C | u | u | a | 17 | 4 | 11 | c | false | <90% | 5908 | ||
| XM_001126792 | LOC728182 | 20 | 38 | U | G | C | C | a | G | U | U | U | c | C | A | A | A | C | C | G | G | u | -39 | 3 | 8 | bc | false | <90% | 582 | ||
| XM_001131658 | LOC732034 | 95 | 113 | U | G | C | C | a | G | U | U | U | c | C | A | A | A | C | C | G | G | c | -39 | 3 | 8 | bc | false | <90% | 624 | ||
| XM_001126744 | LOC728169 | 95 | 113 | U | G | C | C | a | G | U | U | U | c | C | A | A | A | C | C | G | G | c | -39 | 3 | 8 | bc | false | <90% | 633 | ||
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_931896 | LOC348801 | 607 | 625 | C | C | C | u | G | U | U | U | G | A | A | A | A | a | G | G | G | C | c | 38 | 3 | 9 | c | false | <90% | 1025 | ||
| XM_937188 | LOC348801 | 707 | 725 | C | C | C | u | G | U | U | U | G | A | A | A | A | a | G | G | G | C | c | 38 | 3 | 9 | c | false | <90% | 1136 | ||
| XM_379203 | LOC348801 | 1804 | 1822 | C | C | C | u | G | U | U | U | G | A | A | A | A | a | G | G | G | C | c | 38 | 3 | 9 | c | false | <90% | 2233 | ||
| XM_931908 | LOC348801 | 1843 | 1861 | C | C | C | u | G | U | U | U | G | A | A | A | A | a | G | G | G | C | c | 38 | 3 | 9 | c | false | <90% | 2272 | ||
| XM_943217 | LOC348801 | 1861 | 1879 | C | C | C | u | G | U | U | U | G | A | A | A | A | a | G | G | G | C | c | 38 | 3 | 9 | c | false | <90% | 2279 | ||
3 prime UTR Seed matches
Hits to same gene : 0
Hits to other genes : 661
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