Automatic recommendation
OK - siRNA is specific for both sense and antisense (guide) strands
17 hits were found for CAGCUUGAGUCUACACAAA (10 guide strand hits and 7 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_021146 | ANGPTL7 | 1782 | 1800 | u | A | u | C | U | U | G | A | G | U | C | U | A | C | A | C | A | u | u | 70 | 4 | 14 | c | false | <90% | 2255 | ||
| NM_198900 | FMNL3 | 10577 | 10595 | C | A | G | C | U | U | G | A | G | U | C | U | g | C | A | g | A | A | u | 58 | 3 | 12 | false | <90% | 11039 | |||
| NM_175736 | FMNL3 | 10730 | 10748 | C | A | G | C | U | U | G | A | G | U | C | U | g | C | A | g | A | A | u | 58 | 3 | 12 | false | <90% | 11192 | |||
| NM_153687 | IKIP | 405 | 423 | a | A | G | C | U | U | G | A | G | U | C | U | A | C | u | g | A | A | A | 47 | 3 | 13 | c | false | <90% | 2935 | ||
| XM_929947 | LOC646976 | 163 | 181 | u | g | G | C | U | U | G | c | G | U | C | U | A | C | A | C | A | A | c | 19 | 4 | 10 | bc | false | <90% | 2238 | ||
| XM_939981 | LOC646976 | 163 | 181 | u | g | G | C | U | U | G | c | G | U | C | U | A | C | A | C | A | A | c | 19 | 4 | 10 | bc | false | <90% | 2240 | ||
| NM_014379 | KCNV1 | 2490 | 2508 | g | u | a | C | a | U | G | A | G | U | C | U | A | C | A | C | A | A | A | 15 | 4 | 14 | bc | false | <90% | 2944 | ||
| NM_031953 | SNX25 | 2705 | 2723 | a | A | G | u | U | U | G | A | G | a | C | U | A | C | A | C | A | A | A | -21 | 3 | 9 | bc | false | <90% | 3237 | ||
| XM_001128533 | LOC731121 | 296 | 314 | C | A | G | C | U | g | a | A | G | U | C | U | A | C | A | C | A | A | u | -34 | 3 | 11 | bc | false | <90% | 484 | ||
| XM_001128599 | LOC728842 | 296 | 314 | C | A | G | C | U | g | a | A | G | U | C | U | A | C | A | C | A | A | u | -34 | 3 | 11 | bc | false | <90% | 484 | ||
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_033288 | ZNF160 | 59 | 77 | U | c | U | G | U | G | U | A | G | A | C | U | C | A | A | c | C | U | G | 62 | 2 | 13 | c | false | <90% | 4895 | ||
| NM_198893 | ZNF160 | 59 | 77 | U | c | U | G | U | G | U | A | G | A | C | U | C | A | A | c | C | U | G | 62 | 2 | 13 | c | false | <90% | 4980 | ||
| NM_014674 | EDEM1 | 5297 | 5315 | a | U | U | G | U | G | U | A | G | A | C | U | C | A | A | c | a | U | G | 48 | 3 | 14 | c | false | <90% | 6072 | ||
| NM_014923 | FNDC3A | 1881 | 1899 | c | U | U | G | U | G | c | A | G | A | C | U | C | c | A | G | C | U | G | 12 | 3 | 6 | c | false | <90% | 5917 | ||
| NM_001079673 | FNDC3A | 2267 | 2285 | c | U | U | G | U | G | c | A | G | A | C | U | C | c | A | G | C | U | G | 12 | 3 | 6 | c | false | <90% | 6303 | ||
| NM_015477 | SIN3A | 3758 | 3776 | g | g | a | G | U | G | U | A | G | A | u | U | C | A | A | G | C | U | G | 5 | 4 | 8 | c | false | <90% | 5136 | ||
| NM_153487 | MDGA1 | 5595 | 5613 | g | U | U | c | U | G | U | A | G | u | C | U | C | A | A | G | C | U | G | -21 | 3 | 9 | bc | false | <90% | 8907 | ||
3 prime UTR Seed matches
Hits to same gene : 0
Hits to other genes : 2429
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)
Motif found in sense strand
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