Automatic recommendation
OK - siRNA is specific for both sense and antisense (guide) strands
12 hits were found for GAUGAAAGUUGCUCCUAUA (4 guide strand hits and 8 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 | |||||||||||||
| NR_002833 | DPY19L2P1 | 2357 | 2375 | c | A | U | G | A | A | A | G | U | U | G | C | U | a | u | U | A | U | A | 53 | 3 | 12 | c | false | <90% | 3941 | ||
| NM_182554 | C10orf53 | 357 | 375 | G | A | U | G | A | A | A | G | U | U | u | C | U | C | C | U | u | U | g | 10 | 3 | 10 | c | false | <90% | 827 | ||
| NM_024857 | ATAD5 | 2719 | 2737 | a | A | U | G | A | A | A | G | U | c | G | C | U | C | C | U | u | U | A | -8 | 3 | 8 | c | false | <90% | 6245 | ||
| XM_001134002 | C17orf41 | 2740 | 2758 | a | A | U | G | A | A | A | G | U | c | G | C | U | C | C | U | u | U | A | -8 | 3 | 8 | c | false | <90% | 6783 | ||
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 | |||||||||||||
| XR_015822 | LOC731225 | 599 | 617 | c | A | g | A | G | G | A | G | C | A | A | C | U | U | U | C | A | g | C | 75 | 3 | 14 | c | false | <90% | 835 | ||
| XR_015816 | LOC728921 | 599 | 617 | c | A | g | A | G | G | A | G | C | A | A | C | U | U | U | C | A | g | C | 75 | 3 | 14 | c | false | <90% | 835 | ||
| XM_001129608 | CCDC5 | 554 | 572 | c | A | g | A | G | G | A | G | C | A | A | C | U | U | U | C | A | g | C | 75 | 3 | 14 | c | false | <90% | 1002 | ||
| NM_138443 | CCDC5 | 651 | 669 | c | A | g | A | G | G | A | G | C | A | A | C | U | U | U | C | A | g | C | 75 | 3 | 14 | c | false | <90% | 1118 | ||
| NM_007158 | CSDE1 | 377 | 395 | a | A | U | A | c | u | A | G | C | A | A | C | U | U | U | C | A | U | C | -16 | 3 | 13 | bc | false | <90% | 4041 | ||
| NM_001007553 | CSDE1 | 377 | 395 | a | A | U | A | c | u | A | G | C | A | A | C | U | U | U | C | A | U | C | -16 | 3 | 13 | bc | false | <90% | 4115 | ||
| XR_016284 | LOC402422 | 1087 | 1105 | g | A | U | A | G | c | c | G | C | A | A | C | U | U | U | C | A | U | C | -31 | 3 | 12 | bc | false | <90% | 1334 | ||
| XR_018492 | LOC402422 | 1087 | 1105 | g | A | U | A | G | c | c | G | C | A | A | C | U | U | U | C | A | U | C | -31 | 3 | 12 | bc | false | <90% | 1334 | ||
3 prime UTR Seed matches
Hits to same gene : 0
Hits to other genes : 2848
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