Automatic recommendation
OK - siRNA is specific for both sense and antisense (guide) strands
13 hits were found for CACACCAAAUUAUGUAUGU (7 guide strand hits and 6 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_024652 | LRRK1 | 7273 | 7291 | u | A | u | A | C | C | A | A | A | U | U | A | U | G | U | A | U | u | U | 75 | 3 | 14 | c | false | <90% | 7647 | ||
| NM_144632 | TMEM182 | 1521 | 1539 | C | A | u | A | C | C | A | A | A | U | U | A | U | G | U | A | U | a | a | 72 | 3 | 14 | c | false | <90% | 3285 | ||
| NM_016610 | TLR8 | 2486 | 2504 | a | c | C | A | C | C | A | A | A | U | U | A | U | c | U | A | U | G | U | 67 | 3 | 11 | c | false | <90% | 3468 | ||
| NM_138636 | TLR8 | 2349 | 2367 | a | c | C | A | C | C | A | A | A | U | U | A | U | c | U | A | U | G | U | 67 | 3 | 11 | c | false | <90% | 4211 | ||
| NM_001891 | CSN2 | 781 | 799 | u | A | C | c | C | C | A | A | A | U | U | A | a | G | U | A | U | G | U | 50 | 3 | 8 | false | <90% | 1065 | |||
| NM_005898 | CAPRIN1 | 2831 | 2849 | C | A | u | A | C | C | A | A | A | U | U | A | U | G | c | A | U | G | g | 50 | 3 | 11 | c | false | <90% | 5562 | ||
| NM_006933 | SLC5A3 | 3996 | 4014 | g | g | a | A | g | C | A | A | A | U | U | A | U | G | U | A | U | G | U | 15 | 4 | 14 | bc | false | <90% | 11400 | ||
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_178457 | C20orf174 | 9131 | 9149 | A | u | A | U | A | C | A | U | A | A | U | U | U | G | G | U | c | U | G | 65 | 2 | 14 | ac | false | <90% | 9404 | ||
| NM_021163 | RBAK | 3475 | 3493 | A | C | A | U | A | C | A | U | A | A | U | U | U | G | G | a | a | U | u | 45 | 3 | 15 | c | false | <90% | 6551 | ||
| NM_152754 | SEMA3D | 555 | 573 | A | C | A | c | A | C | A | U | A | A | U | U | U | G | G | a | G | U | c | 32 | 3 | 11 | c | false | <90% | 6276 | ||
| NM_001025073 | C3orf17 | 2407 | 2425 | A | C | A | U | u | u | A | U | A | A | U | U | U | G | G | U | G | U | u | -19 | 3 | 12 | bc | false | <90% | 4702 | ||
| NM_001025072 | C3orf17 | 2411 | 2429 | A | C | A | U | u | u | A | U | A | A | U | U | U | G | G | U | G | U | u | -19 | 3 | 12 | bc | false | <90% | 4706 | ||
| NM_015412 | C3orf17 | 2562 | 2580 | A | C | A | U | u | u | A | U | A | A | U | U | U | G | G | U | G | U | u | -19 | 3 | 12 | bc | false | <90% | 4857 | ||
3 prime UTR Seed matches
Hits to same gene : 0
Hits to other genes : 2340
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