Automatic recommendation
OK - siRNA is specific for both sense and antisense (guide) strands
14 hits were found for GAGUCUCAAUACACAAUAA (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_014515 | CNOT2 | 1394 | 1412 | a | c | u | U | C | U | C | A | A | U | A | C | A | C | A | A | U | g | A | 64 | 4 | 14 | c | false | <90% | 3280 | ||
| XM_929970 | TREML3 | 223 | 241 | a | A | G | U | C | U | C | A | u | U | A | C | A | C | A | A | U | c | u | 30 | 4 | 8 | c | false | <90% | 1224 | ||
| XM_941488 | TREML3 | 505 | 523 | a | A | G | U | C | U | C | A | u | U | A | C | A | C | A | A | U | c | u | 30 | 4 | 8 | c | false | <90% | 1506 | ||
| NM_198153 | TREML4 | 339 | 357 | a | A | G | U | C | U | C | A | u | U | A | C | A | C | A | A | U | c | u | 30 | 4 | 8 | c | false | <90% | 2091 | ||
| NM_014388 | C1orf107 | 4962 | 4980 | c | u | c | U | C | U | C | A | A | c | A | C | A | C | A | A | U | A | A | -15 | 4 | 9 | bc | false | <90% | 8463 | ||
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_017610 | RNF111 | 3844 | 3862 | a | U | A | U | U | G | U | G | U | A | U | U | a | A | G | A | C | a | u | 79 | 4 | 11 | false | <90% | 5556 | |||
| XM_929030 | LOC161527 | 4602 | 4620 | g | U | A | U | U | G | g | G | U | A | U | U | G | A | G | A | C | U | C | 31 | 2 | 12 | bc | false | <90% | 7181 | ||
| XM_933066 | LOC643696 | 5143 | 5161 | g | U | A | U | U | G | g | G | U | A | U | U | G | A | G | A | C | U | C | 31 | 2 | 12 | bc | false | <90% | 7191 | ||
| NR_003246 | FLJ40113 | 9760 | 9778 | g | U | A | U | U | G | g | G | U | A | U | U | G | A | G | A | C | U | C | 31 | 2 | 12 | bc | false | <90% | 13179 | ||
| NM_001033002 | RPAIN | 1320 | 1338 | U | U | A | U | U | u | U | G | U | A | U | U | G | A | a | A | C | U | u | 7 | 3 | 8 | c | false | <90% | 1535 | ||
| XM_001130536 | LOC728636 | 4035 | 4053 | g | U | A | c | U | G | g | G | U | A | U | U | G | A | G | A | C | U | C | -5 | 3 | 12 | bc | false | <90% | 8696 | ||
| XM_001130555 | LOC728636 | 4167 | 4185 | g | U | A | c | U | G | g | G | U | A | U | U | G | A | G | A | C | U | C | -5 | 3 | 12 | bc | false | <90% | 8828 | ||
| XM_001130526 | LOC728636 | 4217 | 4235 | g | U | A | c | U | G | g | G | U | A | U | U | G | A | G | A | C | U | C | -5 | 3 | 12 | bc | false | <90% | 8878 | ||
| XM_001130543 | LOC728636 | 6887 | 6905 | g | U | A | c | U | G | g | G | U | A | U | U | G | A | G | A | C | U | C | -5 | 3 | 12 | bc | false | <90% | 11548 | ||
3 prime UTR Seed matches
Hits to same gene : 0
Hits to other genes : 1837
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 sense 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