Automatic recommendation
Not OK - siRNA is not specific
11 hits were found for UUGUAACAUCUUAUAUGAU (8 guide strand hits and 3 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_207445 | FLJ39531 | 2300 | 2318 | c | U | G | U | A | A | C | A | U | C | U | U | A | U | A | U | G | u | U | 95 | 2 | 16 | ac | false | <90% | 3041 | ||
| NM_173471 | SLC25A26 | 500 | 518 | c | U | c | U | A | A | C | A | U | C | U | U | A | U | A | U | G | A | a | 73 | 3 | 15 | bc | false | <90% | 2074 | ||
| NM_001009555 | SH3D19 | 5031 | 5049 | U | U | u | U | A | A | C | A | U | C | U | U | A | U | A | U | u | g | a | 49 | 4 | 13 | c | false | <90% | 5193 | ||
| NM_080725 | SRXN1 | 799 | 817 | a | U | G | U | A | A | C | c | U | C | U | U | A | U | A | U | G | g | a | 28 | 4 | 9 | c | false | <90% | 2580 | ||
| NM_003759 | SLC4A4 | 3720 | 3738 | U | U | G | U | A | A | C | A | c | C | U | U | u | U | A | U | G | A | a | 24 | 3 | 8 | false | <90% | 7586 | |||
| NM_006874 | ELF2 | 2651 | 2669 | a | U | G | U | A | A | C | A | U | u | U | U | A | U | A | U | G | g | U | 12 | 3 | 8 | c | false | <90% | 3171 | ||
| NM_201999 | ELF2 | 2698 | 2716 | a | U | G | U | A | A | C | A | U | u | U | U | A | U | A | U | G | g | U | 12 | 3 | 8 | c | false | <90% | 3218 | ||
| NM_138328 | RHBDL3 | 4605 | 4623 | U | U | G | U | A | A | C | A | U | a | U | U | A | U | u | U | G | A | g | -12 | 3 | 9 | c | false | <90% | 4688 | ||
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_024687 | FLJ23049 | 558 | 576 | A | U | C | A | U | A | U | A | u | G | A | U | G | U | c | A | C | A | A | 15 | 2 | 8 | c | false | <90% | 3240 | ||
| XR_018812 | LOC650496 | 481 | 499 | u | U | C | c | c | A | U | A | A | G | A | U | G | U | U | A | C | A | A | 9 | 3 | 14 | bc | false | <90% | 761 | ||
| XR_015156 | LOC727891 | 481 | 499 | u | U | C | c | c | A | U | A | A | G | A | U | G | U | U | A | C | A | A | 9 | 3 | 14 | bc | false | <90% | 761 | ||
3 prime UTR Seed matches
Hits to same gene : 0
Hits to other genes : 2184
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