Automatic recommendation
OK - siRNA is specific for both sense and antisense (guide) strands
15 hits were found for GAAAUGUAGAGUGGCAGCU (9 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_152529 | GPR155 | 6951 | 6969 | a | A | u | A | U | G | U | A | G | A | G | U | G | a | C | A | G | C | U | 58 | 3 | 10 | c | false | <90% | 7324 | ||
| NM_001033045 | GPR155 | 7100 | 7118 | a | A | u | A | U | G | U | A | G | A | G | U | G | a | C | A | G | C | U | 58 | 3 | 10 | c | false | <90% | 7473 | ||
| NM_006920 | SCN1A | 7082 | 7100 | G | A | A | A | U | G | U | A | G | A | G | U | G | c | a | A | G | C | U | 55 | 2 | 13 | c | false | <90% | 8100 | ||
| NM_012115 | CASP8AP2 | 3061 | 3079 | c | A | A | A | c | G | U | A | G | A | G | U | G | u | C | A | G | C | U | 27 | 3 | 8 | c | false | <90% | 6782 | ||
| XM_941175 | LOC643495 | 325 | 343 | G | A | A | A | U | G | c | A | G | A | G | U | G | G | C | A | u | g | U | 7 | 3 | 9 | c | false | <90% | 698 | ||
| XM_926815 | LOC643495 | 325 | 343 | G | A | A | A | U | G | c | A | G | A | G | U | G | G | C | A | u | g | U | 7 | 3 | 9 | c | false | <90% | 698 | ||
| NR_003149 | GPR98 | 14457 | 14475 | a | A | A | A | U | G | c | A | G | A | G | a | G | G | C | A | G | C | U | -2 | 3 | 7 | false | <90% | 19250 | |||
| NM_032119 | GPR98 | 14540 | 14558 | a | A | A | A | U | G | c | A | G | A | G | a | G | G | C | A | G | C | U | -2 | 3 | 7 | false | <90% | 19333 | |||
| NM_004843 | IL27RA | 2568 | 2586 | G | A | A | A | U | u | g | A | G | A | G | U | G | G | C | A | G | C | U | -29 | 2 | 12 | bc | false | <90% | 3258 | ||
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_033450 | ABCC10 | 3261 | 3279 | A | G | C | U | G | C | C | A | C | U | C | U | g | C | A | U | c | g | C | 63 | 3 | 12 | false | <90% | 5118 | |||
| NM_018423 | STYK1 | 827 | 845 | A | G | C | U | G | C | C | A | C | U | C | U | A | u | A | U | g | g | u | 49 | 4 | 13 | c | false | <90% | 2844 | ||
| NM_004376 | COX15 | 1988 | 2006 | u | G | C | U | G | C | C | A | C | U | C | U | A | C | A | g | g | U | C | 48 | 3 | 14 | c | false | <90% | 2884 | ||
| NM_078470 | COX15 | 3227 | 3245 | u | G | C | U | G | C | C | A | C | U | C | U | A | C | A | g | g | U | C | 48 | 3 | 14 | c | false | <90% | 4081 | ||
| NM_012087 | GTF3C5 | 773 | 791 | A | G | C | U | G | C | C | g | C | U | C | U | A | C | A | U | c | c | C | 11 | 3 | 8 | c | false | <90% | 2380 | ||
| NM_001040000 | MLLT4 | 5493 | 5511 | g | G | C | U | G | C | C | A | u | U | C | a | A | C | A | U | U | U | C | 4 | 3 | 7 | false | <90% | 7551 | |||
3 prime UTR Seed matches
Hits to same gene : 0
Hits to other genes : 4066
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