Automatic recommendation
OK - siRNA is specific for both sense and antisense (guide) strands
16 hits were found for CUGUAACUUAGAAGUAACA (11 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_133378 | TTN | 39503 | 39521 | a | c | G | U | A | A | C | U | U | A | G | A | A | G | U | g | A | C | A | 60 | 3 | 13 | c | false | <90% | 101519 | ||
| NM_133437 | TTN | 20588 | 20606 | a | c | G | U | A | A | C | U | U | A | G | A | A | G | U | g | A | C | A | 60 | 3 | 13 | c | false | <90% | 82604 | ||
| NM_133432 | TTN | 20387 | 20405 | a | c | G | U | A | A | C | U | U | A | G | A | A | G | U | g | A | C | A | 60 | 3 | 13 | c | false | <90% | 82403 | ||
| NM_003319 | TTN | 20012 | 20030 | a | c | G | U | A | A | C | U | U | A | G | A | A | G | U | g | A | C | A | 60 | 3 | 13 | c | false | <90% | 82028 | ||
| NM_020772 | NUFIP2 | 4545 | 4563 | u | U | u | U | A | A | C | U | U | A | G | A | A | G | c | A | A | C | A | 53 | 3 | 11 | c | false | <90% | 4999 | ||
| NM_177948 | ARMCX3 | 1607 | 1625 | u | U | G | U | A | A | u | U | U | A | G | A | A | G | c | A | A | C | A | 6 | 3 | 7 | c | false | <90% | 3318 | ||
| NM_177947 | ARMCX3 | 1656 | 1674 | u | U | G | U | A | A | u | U | U | A | G | A | A | G | c | A | A | C | A | 6 | 3 | 7 | c | false | <90% | 3367 | ||
| NM_016607 | ARMCX3 | 1684 | 1702 | u | U | G | U | A | A | u | U | U | A | G | A | A | G | c | A | A | C | A | 6 | 3 | 7 | c | false | <90% | 3395 | ||
| NM_015268 | DNAJC13 | 185 | 203 | C | a | a | U | A | c | C | U | U | A | G | A | A | G | U | A | A | C | A | 5 | 3 | 13 | bc | false | <90% | 7551 | ||
| XM_001128002 | LOC728153 | 55 | 73 | C | U | G | U | A | A | a | U | U | g | G | A | A | G | U | A | A | C | u | -54 | 3 | 8 | bc | false | <90% | 2160 | ||
| XM_001128014 | LOC728153 | 55 | 73 | C | U | G | U | A | A | a | U | U | g | G | A | A | G | U | A | A | C | u | -54 | 3 | 8 | bc | false | <90% | 2199 | ||
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_025160 | WDR26 | 3774 | 3792 | U | G | a | U | A | C | U | U | C | U | A | A | G | U | U | A | a | A | a | 51 | 3 | 13 | c | false | <90% | 6250 | ||
| NM_015530 | GORASP2 | 2298 | 2316 | U | G | U | U | A | C | a | U | C | U | A | A | a | U | U | A | C | A | a | 18 | 3 | 6 | false | <90% | 2504 | |||
| XM_942193 | DKFZp779B1634 | 732 | 750 | U | G | U | U | g | C | U | U | C | U | A | A | G | U | U | u | C | A | a | 17 | 3 | 10 | c | false | <90% | 2754 | ||
| XM_292717 | DKFZp779B1634 | 732 | 750 | U | G | U | U | g | C | U | U | C | U | A | A | G | U | U | u | C | A | a | 17 | 3 | 10 | c | false | <90% | 2754 | ||
| NM_003410 | ZFX | 4038 | 4056 | U | G | U | U | A | u | U | U | C | U | c | A | G | U | U | A | C | A | G | -24 | 2 | 8 | c | false | <90% | 5811 | ||
3 prime UTR Seed matches
Hits to same gene : 0
Hits to other genes : 1933
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