Automatic recommendation
OK - siRNA is specific for both sense and antisense (guide) strands
11 hits were found for CCAUAUGGGAUGGUGUCAA (5 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_001077523 | AP3D1 | 1040 | 1058 | C | u | c | U | A | U | G | G | G | A | U | G | G | U | G | U | C | c | A | 66 | 3 | 14 | c | false | <90% | 4741 | ||
| NM_003938 | AP3D1 | 1313 | 1331 | C | u | c | U | A | U | G | G | G | A | U | G | G | U | G | U | C | c | A | 66 | 3 | 14 | c | false | <90% | 4863 | ||
| NM_153834 | GPR112 | 662 | 680 | u | g | A | U | A | U | G | G | G | A | U | G | G | U | G | U | g | A | A | 63 | 3 | 14 | ac | false | <90% | 9931 | ||
| NM_007148 | ZNF179 | 1109 | 1127 | C | a | u | U | A | U | G | G | G | A | U | G | G | U | G | c | C | A | A | 42 | 3 | 12 | c | false | <90% | 3209 | ||
| NM_002809 | PSMD3 | 1486 | 1504 | C | C | A | U | c | c | G | G | G | A | U | G | G | U | G | U | C | A | u | -19 | 3 | 12 | bc | false | <90% | 2174 | ||
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 | |||||||||||||
| XM_941377 | KIAA0748 | 763 | 781 | U | U | c | A | C | A | C | C | A | U | C | C | C | A | c | A | U | G | u | 50 | 3 | 11 | c | false | <90% | 3672 | ||
| XM_374983 | KIAA0748 | 763 | 781 | U | U | c | A | C | A | C | C | A | U | C | C | C | A | c | A | U | G | u | 50 | 3 | 11 | c | false | <90% | 3673 | ||
| NM_022474 | MPP5 | 468 | 486 | a | U | G | A | C | A | a | C | A | U | C | C | C | A | U | A | U | G | a | 26 | 3 | 11 | bc | false | <90% | 5375 | ||
| NM_001584 | MPPED2 | 251 | 269 | U | c | G | A | C | c | C | C | A | U | C | C | C | A | U | A | U | G | a | 20 | 3 | 12 | bc | false | <90% | 2272 | ||
| XM_941234 | CASRL1 | 1214 | 1232 | U | U | G | A | C | u | C | C | A | U | C | C | C | A | U | g | U | G | c | 5 | 3 | 9 | c | false | <90% | 2277 | ||
| XM_293581 | CASRL1 | 1262 | 1280 | U | U | G | A | C | u | C | C | A | U | C | C | C | A | U | g | U | G | c | 5 | 3 | 9 | c | false | <90% | 2325 | ||
3 prime UTR Seed matches
Hits to same gene : 0
Hits to other genes : 1378
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