Automatic recommendation
OK - siRNA is specific for both sense and antisense (guide) strands
14 hits were found for GCCAAUCCCGUUGAAAUUC (9 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_015608 | C10orf137 | 2087 | 2105 | u | C | C | A | A | U | C | C | C | G | U | U | a | A | A | A | U | a | u | 79 | 4 | 11 | false | <90% | 4596 | |||
| NM_004360 | CDH1 | 2528 | 2546 | G | C | C | A | A | U | C | C | C | G | a | U | G | A | A | A | U | U | g | 33 | 2 | 10 | c | false | <90% | 4828 | ||
| XM_001129001 | LOC728989 | 1598 | 1616 | a | C | C | A | A | U | u | C | u | G | U | U | G | A | A | A | U | U | C | -28 | 3 | 10 | bc | false | <90% | 1876 | ||
| XM_001133122 | LOC728920 | 1748 | 1766 | a | C | C | A | A | U | u | C | u | G | U | U | G | A | A | A | U | U | C | -28 | 3 | 10 | bc | false | <90% | 2026 | ||
| XM_001132893 | LOC728802 | 1875 | 1893 | a | C | C | A | A | U | u | C | u | G | U | U | G | A | A | A | U | U | C | -28 | 3 | 10 | bc | false | <90% | 2153 | ||
| XM_001132890 | LOC728802 | 1891 | 1909 | a | C | C | A | A | U | u | C | u | G | U | U | G | A | A | A | U | U | C | -28 | 3 | 10 | bc | false | <90% | 2169 | ||
| XM_001133119 | LOC728920 | 1891 | 1909 | a | C | C | A | A | U | u | C | u | G | U | U | G | A | A | A | U | U | C | -28 | 3 | 10 | bc | false | <90% | 2169 | ||
| XM_001132896 | LOC728802 | 2074 | 2092 | a | C | C | A | A | U | u | C | u | G | U | U | G | A | A | A | U | U | C | -28 | 3 | 10 | bc | false | <90% | 2352 | ||
| XM_001133124 | LOC728920 | 2074 | 2092 | a | C | C | A | A | U | u | C | u | G | U | U | G | A | A | A | U | U | C | -28 | 3 | 10 | bc | false | <90% | 2352 | ||
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_015713 | LOC732086 | 733 | 751 | G | A | c | U | U | U | C | A | A | C | G | G | G | A | U | U | a | u | g | 49 | 4 | 13 | c | false | <90% | 1264 | ||
| XR_015726 | LOC729954 | 733 | 751 | G | A | c | U | U | U | C | A | A | C | G | G | G | A | U | U | a | u | g | 49 | 4 | 13 | c | false | <90% | 1264 | ||
| NM_001045 | SLC6A4 | 773 | 791 | G | A | u | U | U | U | C | A | A | a | G | G | G | A | U | U | G | G | u | -7 | 3 | 8 | bc | false | <90% | 2775 | ||
| NM_005858 | AKAP8 | 1451 | 1469 | u | c | c | U | U | U | C | A | A | a | G | G | G | A | U | U | G | G | C | -15 | 4 | 9 | bc | false | <90% | 3545 | ||
| NM_182758 | WDR72 | 2690 | 2708 | G | A | A | U | U | c | C | A | A | g | G | G | G | A | U | U | G | G | a | -51 | 3 | 8 | bc | false | <90% | 5900 | ||
3 prime UTR Seed matches
Hits to same gene : 0
Hits to other genes : 842
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