Automatic recommendation
OK - siRNA is specific for both sense and antisense (guide) strands
12 hits were found for UUGCAGAGAUCUGAAUUCC (2 guide strand hits and 10 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_012137 | DDAH1 | 1684 | 1702 | c | c | c | C | A | G | A | G | A | U | C | U | a | A | A | U | U | C | C | 56 | 4 | 9 | false | <90% | 3949 | |||
| NR_002802 | TncRNA | 3085 | 3103 | a | U | G | C | A | u | A | G | A | U | C | U | G | A | A | U | U | C | a | 29 | 3 | 12 | bc | false | <90% | 14709 | ||
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_133493 | CD109 | 3107 | 3125 | a | G | A | g | U | U | C | A | G | A | U | C | a | C | U | G | C | A | A | 50 | 3 | 8 | false | <90% | 9447 | |||
| NM_017554 | PARP14 | 4189 | 4207 | a | G | A | A | U | c | C | A | G | A | U | C | U | C | U | G | g | A | A | 11 | 3 | 10 | c | false | <90% | 6903 | ||
| NM_007151 | ZNF187 | 617 | 635 | G | G | A | A | U | U | g | A | G | A | U | C | U | C | U | G | g | c | c | 2 | 4 | 9 | c | false | <90% | 3062 | ||
| NM_004288 | PSCDBP | 642 | 660 | G | G | A | g | U | a | C | A | G | A | U | C | U | C | U | G | C | A | g | -5 | 3 | 12 | bc | false | <90% | 2282 | ||
| XM_001132314 | LOC730078 | 376 | 394 | a | G | A | A | U | U | C | A | G | u | U | C | U | C | a | G | C | A | A | -9 | 3 | 8 | c | false | <90% | 839 | ||
| XM_001132439 | LOC732261 | 376 | 394 | a | G | A | A | U | U | C | A | G | u | U | C | U | C | a | G | C | A | A | -9 | 3 | 8 | c | false | <90% | 839 | ||
| NM_206821 | MYBPC1 | 2110 | 2128 | u | G | A | A | U | U | u | u | G | A | U | C | U | C | U | G | C | A | A | -30 | 3 | 11 | bc | false | <90% | 3804 | ||
| NM_206820 | MYBPC1 | 2110 | 2128 | u | G | A | A | U | U | u | u | G | A | U | C | U | C | U | G | C | A | A | -30 | 3 | 11 | bc | false | <90% | 3858 | ||
| NM_206819 | MYBPC1 | 2185 | 2203 | u | G | A | A | U | U | u | u | G | A | U | C | U | C | U | G | C | A | A | -30 | 3 | 11 | bc | false | <90% | 3879 | ||
| NM_002465 | MYBPC1 | 2185 | 2203 | u | G | A | A | U | U | u | u | G | A | U | C | U | C | U | G | C | A | A | -30 | 3 | 11 | bc | false | <90% | 3938 | ||
3 prime UTR Seed matches
Hits to same gene : 0
Hits to other genes : 2755
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