Automatic recommendation
OK - siRNA is specific for both sense and antisense (guide) strands
10 hits were found for UGGUCAAGGAGGUUCCAAC (5 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 | |||||||||||||
| NM_014588 | VSX1 | 1067 | 1085 | U | G | c | U | C | A | A | G | G | A | G | G | c | U | C | C | A | A | C | 70 | 2 | 9 | false | <90% | 1956 | |||
| NM_001012981 | ZKSCAN2 | 2394 | 2412 | g | c | a | U | C | A | A | G | G | A | G | G | a | U | C | C | A | A | C | 56 | 4 | 9 | false | <90% | 7124 | |||
| NM_001025389 | AMPD3 | 1594 | 1612 | U | G | G | U | C | A | A | G | G | A | G | G | U | U | g | C | c | c | g | 44 | 4 | 14 | c | false | <90% | 4334 | ||
| NM_000480 | AMPD3 | 1631 | 1649 | U | G | G | U | C | A | A | G | G | A | G | G | U | U | g | C | c | c | g | 44 | 4 | 14 | c | false | <90% | 4371 | ||
| NM_001025390 | AMPD3 | 1733 | 1751 | U | G | G | U | C | A | A | G | G | A | G | G | U | U | g | C | c | c | g | 44 | 4 | 14 | c | false | <90% | 4473 | ||
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 | |||||||||||||
| XR_019322 | LOC652309 | 679 | 697 | u | g | a | G | G | A | A | C | C | U | C | C | U | U | G | g | C | C | A | 40 | 4 | 12 | c | false | <90% | 1547 | ||
| XM_946373 | LOC654340 | 683 | 701 | u | g | a | G | G | A | A | C | C | U | C | C | U | U | G | g | C | C | A | 40 | 4 | 12 | c | false | <90% | 1761 | ||
| NM_001080506 | FLJ12993 | 469 | 487 | G | U | c | G | G | A | A | C | u | U | C | C | U | U | G | A | C | C | u | 15 | 3 | 9 | bc | false | <90% | 1888 | ||
| XM_001128552 | FLJ12993 | 712 | 730 | G | U | c | G | G | A | A | C | u | U | C | C | U | U | G | A | C | C | u | 15 | 3 | 9 | bc | false | <90% | 2133 | ||
| NM_004446 | EPRS | 605 | 623 | G | U | U | G | G | A | A | a | C | U | C | C | U | U | G | A | g | u | u | 6 | 4 | 8 | c | false | <90% | 5021 | ||
3 prime UTR Seed matches
Hits to same gene : 0
Hits to other genes : 1398
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