Automatic recommendation
OK - siRNA is specific for both sense and antisense (guide) strands
14 hits were found for CAUUGUGGACGUGCAGUAC (14 guide strand hits and 0 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_005115 | MVP | 1992 | 2010 | C | A | g | U | G | U | G | G | A | C | G | U | G | C | A | G | U | c | a | 72 | 3 | 14 | c | false | <90% | 2821 | ||
| NM_017458 | MVP | 2028 | 2046 | C | A | g | U | G | U | G | G | A | C | G | U | G | C | A | G | U | c | a | 72 | 3 | 14 | c | false | <90% | 2857 | ||
| NM_020238 | INCENP | 2566 | 2584 | g | A | c | U | G | U | G | G | A | C | G | U | G | C | A | G | U | c | u | 70 | 4 | 14 | c | false | <90% | 4134 | ||
| NM_001040694 | INCENP | 2578 | 2596 | g | A | c | U | G | U | G | G | A | C | G | U | G | C | A | G | U | c | u | 70 | 4 | 14 | c | false | <90% | 4146 | ||
| NM_194293 | CMYA1 | 4682 | 4700 | C | A | g | U | G | U | G | G | A | C | G | U | G | C | A | G | g | c | C | 54 | 3 | 13 | c | false | <90% | 6451 | ||
| NM_003568 | ANXA9 | 659 | 677 | C | A | U | U | G | U | G | G | A | C | G | U | G | C | u | G | a | c | C | 49 | 3 | 14 | c | false | <90% | 1843 | ||
| NM_002236 | KCNF1 | 1258 | 1276 | C | A | U | U | G | U | G | G | A | C | G | U | G | C | u | G | g | c | C | 49 | 3 | 14 | c | false | <90% | 2304 | ||
| NM_001287 | CLCN7 | 1975 | 1993 | C | A | U | U | G | U | G | G | A | C | G | U | G | C | u | G | a | g | C | 49 | 3 | 14 | c | false | <90% | 3760 | ||
| NM_153487 | MDGA1 | 1545 | 1563 | C | c | g | c | G | U | G | G | A | C | G | U | G | C | A | G | U | A | C | 32 | 3 | 15 | bc | false | <90% | 8907 | ||
| NM_001040071 | LOC650293 | 144 | 162 | g | A | U | U | G | U | G | G | A | C | a | U | G | C | A | G | U | c | g | 29 | 4 | 9 | c | false | <90% | 651 | ||
| XR_018835 | LOC650312 | 144 | 162 | g | A | U | U | G | U | G | G | A | C | a | U | G | C | A | G | U | c | g | 29 | 4 | 9 | c | false | <90% | 848 | ||
| NM_198503 | KCNT2 | 2517 | 2535 | C | A | U | U | G | U | G | a | A | C | G | U | G | C | A | G | a | c | a | 6 | 4 | 8 | c | false | <90% | 5909 | ||
| NM_198516 | GALNTL4 | 1414 | 1432 | C | A | U | U | G | U | G | G | A | C | c | g | G | C | A | G | U | A | C | 4 | 2 | 10 | false | <90% | 2519 | |||
| NM_030768 | ILKAP | 1006 | 1024 | C | A | U | U | G | g | G | G | A | C | G | g | G | C | A | G | U | A | C | 2 | 2 | 7 | false | <90% | 1480 | |||
3 prime UTR Seed matches
Hits to same gene : 0
Hits to other genes : 2461
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