Automatic recommendation
OK - siRNA is specific for both sense and antisense (guide) strands
11 hits were found for GACUACUGCCUCACCCAUA (10 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_017705 | PAQR5 | 2843 | 2861 | G | A | C | U | A | C | U | G | C | C | U | C | u | a | C | C | A | U | u | 65 | 3 | 12 | false | <90% | 4285 | |||
| XM_941833 | LOC90113 | 1479 | 1497 | c | A | C | U | g | C | U | G | C | C | U | C | A | C | C | C | A | U | g | 41 | 3 | 13 | bc | false | <90% | 4155 | ||
| XM_291077 | LOC90113 | 1479 | 1497 | c | A | C | U | g | C | U | G | C | C | U | C | A | C | C | C | A | U | g | 41 | 3 | 13 | bc | false | <90% | 4155 | ||
| NM_004852 | ONECUT2 | 10880 | 10898 | u | c | C | U | A | C | U | G | C | C | a | C | A | C | C | C | A | U | A | 25 | 3 | 8 | c | false | <90% | 16142 | ||
| NM_004913 | C16orf7 | 1758 | 1776 | G | A | C | U | A | C | U | G | C | C | c | C | A | C | C | C | c | a | g | 7 | 4 | 10 | c | false | <90% | 2767 | ||
| XM_928789 | LOC645799 | 516 | 534 | G | A | C | U | A | C | g | a | C | C | U | C | A | C | C | C | A | U | A | -28 | 2 | 11 | bc | false | <90% | 1100 | ||
| XM_937064 | LOC645799 | 516 | 534 | G | A | C | U | A | C | g | a | C | C | U | C | A | C | C | C | A | U | A | -28 | 2 | 11 | bc | false | <90% | 1100 | ||
| NM_001077418 | FLJ22167 | 682 | 700 | G | A | C | U | A | C | g | a | C | C | U | C | A | C | C | C | A | U | A | -28 | 2 | 11 | bc | false | <90% | 2911 | ||
| NM_001077416 | FLJ22167 | 745 | 763 | G | A | C | U | A | C | g | a | C | C | U | C | A | C | C | C | A | U | A | -28 | 2 | 11 | bc | false | <90% | 2974 | ||
| NM_001077419 | FLJ22167 | 805 | 823 | G | A | C | U | A | C | g | a | C | C | U | C | A | C | C | C | A | U | A | -28 | 2 | 11 | bc | false | <90% | 3034 | ||
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_000744 | CHRNA4 | 491 | 509 | U | A | U | G | G | G | U | G | A | a | G | C | A | G | g | A | G | U | g | -12 | 3 | 9 | c | false | <90% | 5540 | ||
3 prime UTR Seed matches
Hits to same gene : 0
Hits to other genes : 871
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