Automatic recommendation
OK - siRNA is specific for both sense and antisense (guide) strands
12 hits were found for CAGCAAUGCAGCUUUGGGU (4 guide strand hits and 8 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_020347 | LZTFL1 | 3191 | 3209 | u | c | a | C | A | A | U | G | C | A | G | C | U | U | U | G | G | u | U | 64 | 4 | 14 | c | false | <90% | 3398 | ||
| NM_022154 | SLC39A8 | 3179 | 3197 | C | A | G | C | A | A | U | G | C | A | G | a | U | U | U | G | G | u | g | 58 | 3 | 11 | false | <90% | 3309 | |||
| XM_001133879 | LOC731918 | 982 | 1000 | C | A | G | C | u | A | U | G | C | A | G | C | U | U | g | G | G | G | c | 18 | 3 | 9 | c | false | <90% | 2216 | ||
| NM_006395 | ATG7 | 1510 | 1528 | C | A | u | C | A | A | U | G | C | u | G | C | U | U | U | G | G | G | a | -7 | 3 | 8 | bc | false | <90% | 2396 | ||
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_198455 | SSPO | 8353 | 8371 | u | C | C | C | A | A | A | G | C | U | G | C | c | U | U | G | C | c | c | 79 | 4 | 11 | false | <90% | 15580 | |||
| XR_015150 | LOC730534 | 554 | 572 | c | u | C | C | A | A | A | G | C | U | G | C | A | U | U | G | a | U | G | 63 | 3 | 14 | ac | false | <90% | 1197 | ||
| XR_015995 | LOC729564 | 554 | 572 | c | u | C | C | A | A | A | G | C | U | G | C | A | U | U | G | a | U | G | 63 | 3 | 14 | ac | false | <90% | 1197 | ||
| NM_022162 | NOD2 | 454 | 472 | c | C | C | C | c | A | A | G | C | U | G | C | A | U | g | G | C | U | G | 21 | 3 | 9 | c | false | <90% | 4485 | ||
| NM_144670 | A2ML1 | 3335 | 3353 | u | g | u | C | A | c | A | G | C | U | G | C | A | U | U | G | C | U | G | 3 | 4 | 13 | bc | false | <90% | 5123 | ||
| NM_001077262 | UBXD5 | 1176 | 1194 | g | C | C | C | A | A | A | G | C | a | G | C | A | c | U | G | C | U | G | -4 | 3 | 8 | c | false | <90% | 1384 | ||
| NM_145345 | UBXD5 | 1656 | 1674 | g | C | C | C | A | A | A | G | C | a | G | C | A | c | U | G | C | U | G | -4 | 3 | 8 | c | false | <90% | 1864 | ||
| NM_183008 | UBXD5 | 1661 | 1679 | g | C | C | C | A | A | A | G | C | a | G | C | A | c | U | G | C | U | G | -4 | 3 | 8 | c | false | <90% | 1869 | ||
3 prime UTR Seed matches
Hits to same gene : 0
Hits to other genes : 1970
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