Automatic recommendation
OK - siRNA is specific for both sense and antisense (guide) strands
14 hits were found for UUGUAGGCUUGAUGUGGCU (5 guide strand hits and 9 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_003559 | PIP5K2B | 2967 | 2985 | U | U | G | g | A | G | G | C | U | U | G | A | U | G | U | G | G | g | U | 60 | 2 | 13 | c | false | <90% | 5732 | ||
| XM_939208 | LOC648149 | 1613 | 1631 | U | U | G | U | A | G | G | C | U | U | a | A | U | G | U | G | c | a | g | 7 | 4 | 10 | c | false | <90% | 2989 | ||
| XM_001133680 | LOC648149 | 1613 | 1631 | U | U | G | U | A | G | G | C | U | U | a | A | U | G | U | G | c | a | g | 7 | 4 | 10 | c | false | <90% | 2989 | ||
| NM_170706 | NMNAT2 | 1597 | 1615 | U | U | G | U | A | G | u | C | U | U | G | A | U | G | U | G | c | u | c | 2 | 4 | 9 | c | false | <90% | 5465 | ||
| NM_015039 | NMNAT2 | 1812 | 1830 | U | U | G | U | A | G | u | C | U | U | G | A | U | G | U | G | c | u | c | 2 | 4 | 9 | c | false | <90% | 5680 | ||
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_014715 | RICS | 2706 | 2724 | A | G | C | C | A | C | A | U | C | A | A | G | C | a | U | A | u | u | u | 49 | 4 | 13 | c | false | <90% | 6480 | ||
| NM_004311 | ARL3 | 285 | 303 | A | G | C | C | A | C | A | U | C | A | c | a | C | C | U | A | C | A | c | 0 | 3 | 10 | false | <90% | 3891 | |||
| NM_022059 | CXCL16 | 1367 | 1385 | u | a | C | C | A | C | A | U | C | c | A | G | C | C | U | A | C | A | c | -1 | 4 | 8 | bc | false | <90% | 2249 | ||
| NM_181483 | C18orf1 | 2143 | 2161 | c | c | C | C | A | C | A | U | C | c | A | G | C | C | U | A | C | A | c | -1 | 4 | 8 | bc | false | <90% | 8031 | ||
| NM_004338 | C18orf1 | 2197 | 2215 | c | c | C | C | A | C | A | U | C | c | A | G | C | C | U | A | C | A | c | -1 | 4 | 8 | bc | false | <90% | 8085 | ||
| NM_181482 | C18orf1 | 2734 | 2752 | c | c | C | C | A | C | A | U | C | c | A | G | C | C | U | A | C | A | c | -1 | 4 | 8 | bc | false | <90% | 8617 | ||
| NM_181481 | C18orf1 | 2788 | 2806 | c | c | C | C | A | C | A | U | C | c | A | G | C | C | U | A | C | A | c | -1 | 4 | 8 | bc | false | <90% | 8676 | ||
| NM_001003675 | C18orf1 | 3002 | 3020 | c | c | C | C | A | C | A | U | C | c | A | G | C | C | U | A | C | A | c | -1 | 4 | 8 | bc | false | <90% | 8890 | ||
| NM_001003674 | C18orf1 | 3056 | 3074 | c | c | C | C | A | C | A | U | C | c | A | G | C | C | U | A | C | A | c | -1 | 4 | 8 | bc | false | <90% | 8944 | ||
3 prime UTR Seed matches
Hits to same gene : 0
Hits to other genes : 1526
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