Automatic recommendation
OK - siRNA is specific for both sense and antisense (guide) strands
12 hits were found for UCACUCACCAACCUCCUGU (8 guide strand hits and 4 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_014938 | MLXIP | 2995 | 3013 | U | C | A | g | U | C | A | C | C | A | A | C | C | U | C | C | U | c | U | 60 | 2 | 13 | c | false | <90% | 5400 | ||
| NM_020443 | NAV1 | 615 | 633 | U | C | A | C | U | C | A | C | C | A | A | C | C | U | C | u | c | u | U | 47 | 3 | 15 | c | false | <90% | 11365 | ||
| NM_017564 | STAB2 | 7153 | 7171 | U | C | A | C | U | C | A | C | a | A | A | C | u | U | C | C | U | G | a | 24 | 3 | 8 | false | <90% | 8266 | |||
| NM_000669 | ADH1C | 44 | 62 | g | u | A | C | U | C | A | C | C | A | g | C | C | U | C | C | U | G | g | 20 | 4 | 8 | c | false | <90% | 1497 | ||
| NM_173619 | MGC34761 | 117 | 135 | U | C | A | C | U | C | A | C | C | A | g | C | C | U | C | C | c | u | c | 7 | 4 | 10 | c | false | <90% | 2100 | ||
| NM_014858 | TMCC2 | 2533 | 2551 | U | C | c | C | U | C | A | C | C | u | A | C | C | U | C | C | U | G | g | -7 | 3 | 8 | bc | false | <90% | 3792 | ||
| XM_001133526 | LOC729481 | 377 | 395 | g | C | A | C | U | C | u | C | C | A | g | C | C | U | C | C | U | G | U | -29 | 3 | 8 | c | false | <90% | 579 | ||
| XM_001133716 | LOC731689 | 377 | 395 | g | C | A | C | U | C | u | C | C | A | g | C | C | U | C | C | U | G | U | -29 | 3 | 8 | c | false | <90% | 579 | ||
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_000859 | HMGCR | 3949 | 3967 | c | C | A | G | G | A | G | G | U | U | G | G | U | G | A | c | U | G | A | 71 | 2 | 14 | c | false | <90% | 4471 | ||
| NM_199368 | TRPC4AP | 1519 | 1537 | A | C | A | G | G | A | G | u | U | U | G | G | U | G | u | G | U | G | A | 13 | 2 | 7 | c | false | <90% | 3165 | ||
| NM_015638 | TRPC4AP | 1543 | 1561 | A | C | A | G | G | A | G | u | U | U | G | G | U | G | u | G | U | G | A | 13 | 2 | 7 | c | false | <90% | 3189 | ||
| NM_152317 | DEPDC4 | 589 | 607 | A | C | A | G | G | A | G | a | U | U | G | G | U | G | A | G | g | a | A | 11 | 3 | 8 | c | false | <90% | 1155 | ||
3 prime UTR Seed matches
Hits to same gene : 0
Hits to other genes : 2098
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