Automatic recommendation
OK - siRNA is specific for both sense and antisense (guide) strands
13 hits were found for CAUUCUAUAUAAGAGAGAA (7 guide strand hits and 6 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_004936 | CDKN2B | 3184 | 3202 | C | A | U | U | C | U | A | U | A | U | A | A | a | A | G | A | a | g | u | 58 | 4 | 12 | false | <90% | 3878 | |||
| NM_078487 | CDKN2B | 3307 | 3325 | C | A | U | U | C | U | A | U | A | U | A | A | a | A | G | A | a | g | u | 58 | 4 | 12 | false | <90% | 4001 | |||
| NR_003135 | CEP170L | 44105 | 44123 | C | A | U | U | u | U | A | U | A | U | A | A | G | A | G | A | a | A | A | 25 | 2 | 11 | c | false | <90% | 90477 | ||
| NM_030641 | APOL6 | 6687 | 6705 | a | A | U | U | u | U | A | U | A | U | A | A | G | A | a | A | G | A | A | 21 | 3 | 9 | c | false | <90% | 10156 | ||
| NM_021827 | CCDC81 | 366 | 384 | C | A | U | U | C | c | A | U | A | U | A | A | G | A | a | A | G | A | A | 12 | 2 | 8 | c | false | <90% | 2510 | ||
| XR_015368 | LOC728735 | 863 | 881 | C | A | U | U | C | U | A | U | A | g | A | A | G | A | G | g | G | A | u | -13 | 3 | 9 | c | false | <90% | 4286 | ||
| NM_014562 | OTX1 | 1552 | 1570 | C | A | U | U | C | U | A | U | A | c | A | g | G | A | G | A | G | A | u | -21 | 3 | 9 | false | <90% | 2176 | |||
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_207361 | FREM2 | 9141 | 9159 | U | U | C | a | C | U | C | U | U | A | U | A | U | A | G | A | u | U | u | 34 | 3 | 12 | c | false | <90% | 16179 | ||
| NM_021950 | MS4A1 | 1192 | 1210 | U | U | C | U | C | U | C | U | U | A | c | A | U | u | G | A | A | U | G | 19 | 2 | 10 | c | false | <90% | 3331 | ||
| NM_152866 | MS4A1 | 1455 | 1473 | U | U | C | U | C | U | C | U | U | A | c | A | U | u | G | A | A | U | G | 19 | 2 | 10 | c | false | <90% | 3594 | ||
| XR_015867 | LOC730239 | 775 | 793 | U | U | C | U | C | U | C | U | U | A | g | A | U | A | c | A | A | U | a | 9 | 3 | 10 | c | false | <90% | 1069 | ||
| XR_015222 | LOC730681 | 775 | 793 | U | U | C | U | C | U | C | U | U | A | g | A | U | A | c | A | A | U | a | 9 | 3 | 10 | c | false | <90% | 1069 | ||
| NM_012367 | OR2B6 | 822 | 840 | U | U | C | U | C | U | C | U | U | c | U | A | U | g | G | A | A | U | c | -7 | 3 | 9 | c | false | <90% | 942 | ||
3 prime UTR Seed matches
Hits to same gene : 0
Hits to other genes : 1898
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