Automatic recommendation
OK - siRNA is specific for both sense and antisense (guide) strands
12 hits were found for CGCUCAGUAAGGACACCAG (5 guide strand hits and 7 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_001039762 | FLJ45557 | 558 | 576 | u | G | g | U | C | A | G | U | A | A | G | G | A | C | A | C | C | g | G | 75 | 3 | 14 | c | false | <90% | 4408 | ||
| NM_001031672 | LOC606495 | 580 | 598 | g | G | C | U | C | A | c | U | A | A | G | G | A | C | A | C | C | u | a | 24 | 4 | 10 | c | false | <90% | 3551 | ||
| NM_173662 | RNF175 | 756 | 774 | C | u | C | U | C | A | G | g | A | A | G | G | A | C | A | C | C | A | c | 21 | 3 | 10 | bc | false | <90% | 1605 | ||
| NM_014676 | PUM1 | 1598 | 1616 | g | G | C | U | C | A | G | c | A | A | G | G | A | C | A | g | C | A | G | 9 | 3 | 7 | c | false | <90% | 5410 | ||
| NM_001020658 | PUM1 | 1598 | 1616 | g | G | C | U | C | A | G | c | A | A | G | G | A | C | A | g | C | A | G | 9 | 3 | 7 | c | false | <90% | 5416 | ||
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_014870 | ZBTB40 | 2223 | 2241 | u | U | G | G | U | G | U | C | C | U | U | A | C | U | a | A | G | g | a | 65 | 4 | 13 | c | false | <90% | 8704 | ||
| NM_001083621 | ZBTB40 | 2511 | 2529 | u | U | G | G | U | G | U | C | C | U | U | A | C | U | a | A | G | g | a | 65 | 4 | 13 | c | false | <90% | 8992 | ||
| XR_016324 | LOC643860 | 83 | 101 | C | U | G | G | U | a | U | C | C | U | U | A | C | U | G | A | u | C | u | 8 | 3 | 10 | c | false | <90% | 1402 | ||
| XR_016258 | LOC442416 | 83 | 101 | C | U | G | G | U | a | U | C | C | U | U | A | C | U | G | A | u | C | u | 8 | 3 | 10 | c | false | <90% | 1426 | ||
| NM_020396 | BCL2L10 | 470 | 488 | C | U | G | G | U | G | g | C | C | U | U | g | C | U | G | A | G | C | u | -5 | 3 | 6 | false | <90% | 887 | |||
| XM_943623 | LOC649217 | 772 | 790 | a | U | G | G | c | G | U | C | C | U | c | A | C | U | G | A | G | C | G | -14 | 3 | 8 | c | false | <90% | 1275 | ||
| NM_000170 | GLDC | 912 | 930 | C | U | G | G | a | G | U | C | C | U | c | A | C | U | G | A | G | C | u | -17 | 3 | 7 | c | false | <90% | 3820 | ||
3 prime UTR Seed matches
Hits to same gene : 0
Hits to other genes : 550
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