Automatic recommendation
OK - siRNA is specific for both sense and antisense (guide) strands
9 hits were found for AACAGCAUAUUGACGCUGG (4 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_012231 | PRDM2 | 6530 | 6548 | A | A | C | A | G | C | A | U | A | U | U | G | A | C | a | C | g | u | u | 44 | 4 | 14 | c | false | <90% | 7958 | ||
| NM_020414 | DDX24 | 1310 | 1328 | A | A | C | A | G | C | A | c | A | U | U | G | A | u | G | C | U | G | u | 13 | 3 | 7 | c | false | <90% | 2967 | ||
| NM_000068 | CACNA1A | 6029 | 6047 | A | A | C | A | G | C | A | g | A | U | g | G | A | C | G | C | U | G | a | -28 | 3 | 7 | c | false | <90% | 7807 | ||
| NM_023035 | CACNA1A | 6029 | 6047 | A | A | C | A | G | C | A | g | A | U | g | G | A | C | G | C | U | G | a | -28 | 3 | 7 | c | false | <90% | 7812 | ||
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_001126669 | LOC442064 | 659 | 677 | C | u | A | G | a | G | U | C | A | A | U | A | U | G | C | U | G | U | a | 32 | 3 | 13 | bc | false | <90% | 1231 | ||
| XM_497897 | LOC442064 | 659 | 677 | C | u | A | G | a | G | U | C | A | A | U | A | U | G | C | U | G | U | a | 32 | 3 | 13 | bc | false | <90% | 1231 | ||
| NM_032906 | PIGY | 769 | 787 | C | u | A | G | a | G | U | C | A | A | U | A | U | G | C | U | G | U | a | 32 | 3 | 13 | bc | false | <90% | 1353 | ||
| NM_001042616 | PIGY | 769 | 787 | C | u | A | G | a | G | U | C | A | A | U | A | U | G | C | U | G | U | a | 32 | 3 | 13 | bc | false | <90% | 1353 | ||
| NM_138468 | ICA1L | 7432 | 7450 | C | u | A | G | a | G | U | C | A | A | U | A | U | G | C | U | G | U | a | 32 | 3 | 13 | bc | false | <90% | 7996 | ||
3 prime UTR Seed matches
Hits to same gene : 0
Hits to other genes : 2548
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