Automatic recommendation
OK - siRNA is specific for both sense and antisense (guide) strands
16 hits were found for GAUCUGUUCCACCAUUGAA (2 guide strand hits and 14 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_020898 | CALCOCO1 | 2657 | 2675 | u | u | U | C | U | G | U | U | C | C | c | C | C | A | U | U | G | A | c | 20 | 4 | 8 | c | false | <90% | 3003 | ||
| NM_000122 | ERCC3 | 1232 | 1250 | G | A | U | g | U | G | g | U | C | C | A | C | C | A | U | U | G | A | c | -8 | 3 | 11 | bc | false | <90% | 2751 | ||
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_152517 | TTC30B | 1354 | 1372 | U | c | C | A | A | U | G | G | U | G | G | A | A | a | A | G | A | U | C | 69 | 2 | 11 | c | false | <90% | 2652 | ||
| NM_012309 | SHANK2 | 6565 | 6583 | U | U | u | A | A | U | G | G | U | G | G | A | A | C | A | a | A | U | g | 49 | 3 | 12 | c | false | <90% | 8778 | ||
| NM_001010888 | ZC3H12B | 3935 | 3953 | a | U | C | A | u | U | G | G | U | G | G | A | A | C | A | G | A | a | u | 38 | 4 | 12 | c | false | <90% | 7024 | ||
| NM_002647 | PIK3C3 | 2674 | 2692 | U | g | C | A | g | U | G | G | U | G | G | A | A | C | A | G | A | U | u | 32 | 3 | 13 | bc | false | <90% | 3083 | ||
| NM_001467 | SLC37A4 | 337 | 355 | a | U | C | A | u | U | G | G | U | G | G | A | A | g | A | G | A | U | C | 27 | 3 | 8 | c | false | <90% | 2090 | ||
| NM_178539 | FAM19A2 | 1773 | 1791 | U | U | C | A | A | U | a | G | U | G | G | A | A | C | A | G | A | a | a | 26 | 3 | 10 | c | false | <90% | 4069 | ||
| NM_003901 | SGPL1 | 796 | 814 | U | U | C | A | A | U | G | G | g | G | G | A | c | C | A | G | A | U | u | 24 | 3 | 8 | false | <90% | 4701 | |||
| NM_014637 | MTFR1 | 1589 | 1607 | U | U | C | A | A | U | G | a | U | G | G | A | A | C | A | G | c | U | g | 9 | 3 | 8 | c | false | <90% | 2691 | ||
| NM_054112 | DEFB118 | 104 | 122 | a | a | a | A | A | U | G | c | U | G | G | A | A | C | A | G | A | U | C | 4 | 4 | 11 | bc | false | <90% | 589 | ||
| NM_003692 | TMEFF1 | 1843 | 1861 | a | g | u | A | A | U | G | a | U | G | G | A | A | C | A | G | A | U | C | 4 | 4 | 11 | bc | false | <90% | 2299 | ||
| NM_014413 | EIF2AK1 | 1068 | 1086 | U | U | C | A | A | U | u | G | U | G | G | A | A | C | A | G | c | a | g | 2 | 4 | 9 | c | false | <90% | 2813 | ||
| NM_001039712 | DEDD | 1756 | 1774 | U | U | C | A | A | a | G | G | a | G | G | A | A | C | A | G | A | U | a | -28 | 3 | 9 | bc | false | <90% | 2300 | ||
| NM_001039711 | DEDD | 1785 | 1803 | U | U | C | A | A | a | G | G | a | G | G | A | A | C | A | G | A | U | a | -28 | 3 | 9 | bc | false | <90% | 2329 | ||
| NM_032998 | DEDD | 1818 | 1836 | U | U | C | A | A | a | G | G | a | G | G | A | A | C | A | G | A | U | a | -28 | 3 | 9 | bc | false | <90% | 2362 | ||
3 prime UTR Seed matches
Hits to same gene : 0
Hits to other genes : 1790
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