Automatic recommendation
OK - siRNA is specific for both sense and antisense (guide) strands
17 hits were found for CCUAUAUGGAGAUGAGCAA (6 guide strand hits and 11 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_000170 | GLDC | 3166 | 3184 | C | a | U | A | U | A | U | G | G | A | G | A | U | c | A | G | C | A | c | 64 | 3 | 11 | c | false | <90% | 3820 | ||
| NM_145017 | C11orf66 | 866 | 884 | C | C | U | A | c | A | U | G | G | A | G | A | U | G | A | G | u | u | c | 17 | 4 | 11 | c | false | <90% | 1531 | ||
| XR_017509 | LOC647189 | 499 | 517 | C | C | U | A | c | A | U | G | G | A | G | c | U | G | A | G | C | A | g | 9 | 3 | 6 | false | <90% | 636 | |||
| NM_005211 | CSF1R | 2457 | 2475 | C | C | U | A | U | g | U | G | G | A | G | A | U | G | A | G | g | c | c | 5 | 4 | 10 | c | false | <90% | 3985 | ||
| XR_018178 | LOC642929 | 532 | 550 | C | C | U | A | U | g | U | G | G | A | G | c | U | G | A | G | C | A | g | -2 | 3 | 6 | false | <90% | 1267 | |||
| NM_002609 | PDGFRB | 2685 | 2703 | g | C | U | A | c | A | U | G | G | A | c | A | U | G | A | G | C | A | A | -14 | 3 | 8 | c | false | <90% | 5718 | ||
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 | |||||||||||||
| XM_001133055 | LOC728760 | 1503 | 1521 | U | U | G | C | U | C | A | U | C | U | C | C | A | a | A | U | A | a | a | 72 | 3 | 13 | c | false | <90% | 1777 | ||
| NM_182497 | KRT40 | 1539 | 1557 | U | U | G | C | U | C | A | U | C | U | C | C | A | a | A | U | A | a | a | 72 | 3 | 13 | c | false | <90% | 1813 | ||
| NM_020461 | TUBGCP6 | 2234 | 2252 | g | U | G | C | U | C | A | U | C | U | C | C | A | a | A | g | A | G | G | 52 | 3 | 12 | c | false | <90% | 6040 | ||
| NM_022342 | KIF9 | 2409 | 2427 | U | U | G | C | U | C | A | U | C | U | C | C | A | c | A | g | A | G | c | 49 | 3 | 13 | c | false | <90% | 2509 | ||
| NM_182902 | KIF9 | 2652 | 2670 | U | U | G | C | U | C | A | U | C | U | C | C | A | c | A | g | A | G | c | 49 | 3 | 13 | c | false | <90% | 2764 | ||
| NM_181310 | IL22RA2 | 1701 | 1719 | U | U | c | C | U | C | A | U | C | U | C | u | A | U | A | U | A | G | G | 46 | 2 | 8 | false | <90% | 2644 | |||
| NM_181309 | IL22RA2 | 1871 | 1889 | U | U | c | C | U | C | A | U | C | U | C | u | A | U | A | U | A | G | G | 46 | 2 | 8 | false | <90% | 2814 | |||
| NM_052962 | IL22RA2 | 1967 | 1985 | U | U | c | C | U | C | A | U | C | U | C | u | A | U | A | U | A | G | G | 46 | 2 | 8 | false | <90% | 2910 | |||
| XR_018255 | LOC643004 | 668 | 686 | U | U | c | u | U | C | A | U | C | U | C | C | A | U | A | U | A | G | c | 38 | 3 | 14 | bc | false | <90% | 2694 | ||
| XM_940123 | LOC643475 | 1134 | 1152 | U | U | G | C | U | C | A | a | C | U | C | C | A | U | A | U | g | a | a | 6 | 4 | 8 | c | false | <90% | 4902 | ||
| XM_928745 | LOC643475 | 1134 | 1152 | U | U | G | C | U | C | A | a | C | U | C | C | A | U | A | U | g | a | a | 6 | 4 | 8 | c | false | <90% | 4904 | ||
3 prime UTR Seed matches
Hits to same gene : 0
Hits to other genes : 1119
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