Automatic recommendation
OK - siRNA is specific for both sense and antisense (guide) strands
11 hits were found for CAGCCCUAUGUGUUCAUUA (10 guide strand hits and 1 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 | |||||||||||||
| XM_499123 | FLJ46284 | 1796 | 1814 | a | A | c | C | C | C | U | A | U | G | U | G | U | U | C | A | U | a | A | 75 | 3 | 14 | c | false | <90% | 3370 | ||
| XM_942952 | FLJ46284 | 1796 | 1814 | a | A | c | C | C | C | U | A | U | G | U | G | U | U | C | A | U | a | A | 75 | 3 | 14 | c | false | <90% | 3370 | ||
| NM_001001959 | OR11L1 | 646 | 664 | g | g | G | C | C | C | U | A | U | G | U | u | U | U | C | A | U | U | g | 47 | 4 | 9 | false | <90% | 969 | |||
| NM_003922 | HERC1 | 5424 | 5442 | u | u | G | C | C | C | U | A | a | G | U | G | U | U | C | A | U | U | A | 26 | 3 | 10 | bc | false | <90% | 15216 | ||
| NM_012341 | GTPBP4 | 657 | 675 | C | A | G | C | C | C | U | A | U | G | c | G | U | U | C | A | c | a | A | 12 | 3 | 10 | c | false | <90% | 2537 | ||
| NM_001077206 | SEC31A | 1434 | 1452 | C | A | G | C | a | C | c | A | U | G | U | G | U | U | C | A | U | U | A | -17 | 2 | 12 | bc | false | <90% | 3902 | ||
| NM_016211 | SEC31A | 1431 | 1449 | C | A | G | C | a | C | c | A | U | G | U | G | U | U | C | A | U | U | A | -17 | 2 | 12 | bc | false | <90% | 4124 | ||
| NM_001077208 | SEC31A | 1434 | 1452 | C | A | G | C | a | C | c | A | U | G | U | G | U | U | C | A | U | U | A | -17 | 2 | 12 | bc | false | <90% | 4199 | ||
| NM_014933 | SEC31A | 1431 | 1449 | C | A | G | C | a | C | c | A | U | G | U | G | U | U | C | A | U | U | A | -17 | 2 | 12 | bc | false | <90% | 4241 | ||
| NM_001077207 | SEC31A | 1434 | 1452 | C | A | G | C | a | C | c | A | U | G | U | G | U | U | C | A | U | U | A | -17 | 2 | 12 | bc | false | <90% | 4244 | ||
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_052885 | SLC2A13 | 4904 | 4922 | a | u | A | U | a | A | A | C | A | C | A | U | A | G | G | G | C | U | G | 35 | 3 | 14 | bc | false | <90% | 7003 | ||
3 prime UTR Seed matches
Hits to same gene : 0
Hits to other genes : 3936
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)
Motif found in guide strand
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