Automatic recommendation
Warning - siRNA is specific for only the antisense (guide) strand
8 hits were found for CGAGGAUAAUAUUGGCAAA (3 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_015313 | ARHGEF12 | 2836 | 2854 | g | u | u | G | G | A | U | A | A | U | A | U | U | G | c | C | A | A | A | 42 | 4 | 11 | c | false | <90% | 9501 | ||
| NM_031371 | ARID4B | 2421 | 2439 | C | a | u | G | G | A | U | A | A | U | A | a | U | G | G | C | A | A | A | 35 | 3 | 8 | false | <90% | 5809 | |||
| NM_016374 | ARID4B | 2679 | 2697 | C | a | u | G | G | A | U | A | A | U | A | a | U | G | G | C | A | A | A | 35 | 3 | 8 | false | <90% | 6067 | |||
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_003296 | CRISP2 | 736 | 754 | U | U | U | G | C | C | A | A | U | A | U | U | g | U | C | C | U | g | c | 81 | 3 | 12 | false | <90% | 1406 | |||
| NM_006061 | CRISP3 | 517 | 535 | U | U | U | G | C | C | A | A | U | A | U | U | g | U | C | C | U | g | c | 81 | 3 | 12 | false | <90% | 2128 | |||
| NM_032487 | ARPM1 | 1247 | 1265 | U | U | U | u | C | C | A | A | U | A | U | U | A | U | C | C | U | u | G | 60 | 2 | 13 | c | false | <90% | 2001 | ||
| NM_001039580 | MAP9 | 2243 | 2261 | U | U | U | G | C | C | A | A | U | A | U | U | A | g | C | C | a | u | a | 49 | 4 | 13 | c | false | <90% | 7333 | ||
| NM_145044 | ZNF501 | 2875 | 2893 | U | U | U | G | C | a | A | A | U | A | U | U | u | U | C | C | U | C | c | 21 | 3 | 6 | false | <90% | 3081 | |||
3 prime UTR Seed matches
Hits to same gene : 0
Hits to other genes : 324
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