Automatic recommendation
OK - siRNA is specific for both sense and antisense (guide) strands
10 hits were found for GAACUACCAUUCAAGGUCU (8 guide strand hits and 2 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_152539 | C3orf30 | 1770 | 1788 | u | A | A | C | U | A | C | C | A | U | U | C | A | A | G | u | U | u | U | 69 | 3 | 14 | c | false | <90% | 1814 | ||
| NM_022037 | TIA1 | 964 | 982 | G | u | A | C | U | A | C | C | A | U | U | g | A | A | G | G | U | C | a | 49 | 3 | 9 | false | <90% | 2357 | |||
| NM_022173 | TIA1 | 997 | 1015 | G | u | A | C | U | A | C | C | A | U | U | g | A | A | G | G | U | C | a | 49 | 3 | 9 | false | <90% | 2390 | |||
| NM_020193 | C11orf30 | 1906 | 1924 | G | A | A | C | g | A | C | C | A | U | U | C | A | A | G | G | c | C | U | 25 | 2 | 11 | c | false | <90% | 5518 | ||
| NM_000035 | ALDOB | 490 | 508 | a | A | A | C | c | A | C | C | A | U | U | C | A | A | G | G | g | C | U | 23 | 3 | 11 | c | false | <90% | 1669 | ||
| NM_181508 | HPS5 | 209 | 227 | u | A | g | C | U | A | C | C | A | g | U | C | A | A | G | G | U | C | U | -4 | 3 | 9 | bc | false | <90% | 4536 | ||
| NM_007216 | HPS5 | 396 | 414 | u | A | g | C | U | A | C | C | A | g | U | C | A | A | G | G | U | C | U | -4 | 3 | 9 | bc | false | <90% | 4723 | ||
| NM_181507 | HPS5 | 553 | 571 | u | A | g | C | U | A | C | C | A | g | U | C | A | A | G | G | U | C | U | -4 | 3 | 9 | bc | false | <90% | 4880 | ||
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_022106 | C20orf177 | 3419 | 3437 | A | G | A | C | C | U | U | G | A | A | U | G | G | U | u | G | a | g | g | 44 | 4 | 14 | c | false | <90% | 3825 | ||
| NM_016621 | PHF21A | 3405 | 3423 | A | G | A | C | C | U | U | G | c | A | U | G | G | U | A | G | a | g | u | 8 | 4 | 8 | c | false | <90% | 3692 | ||
3 prime UTR Seed matches
Hits to same gene : 0
Hits to other genes : 917
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