Automatic recommendation
OK - siRNA is specific for both sense and antisense (guide) strands
14 hits were found for UUCCUAUACUGGCUGCUUA (11 guide strand hits and 3 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_178839 | LRRTM1 | 295 | 313 | U | g | u | C | U | A | U | A | C | U | G | G | C | U | G | C | U | g | A | 66 | 3 | 14 | c | false | <90% | 2217 | ||
| NM_001005181 | OR56B4 | 494 | 512 | U | g | C | C | U | A | U | A | C | U | G | G | C | U | G | C | c | c | A | 62 | 3 | 14 | ac | false | <90% | 960 | ||
| NM_001964 | EGR1 | 663 | 681 | c | a | C | C | U | A | U | A | C | U | G | G | C | c | G | C | U | U | u | 62 | 4 | 11 | c | false | <90% | 3136 | ||
| NM_178505 | TMEM26 | 3688 | 3706 | c | U | C | u | U | A | U | A | C | U | G | G | C | U | G | C | U | U | u | 56 | 3 | 14 | bc | false | <90% | 5170 | ||
| NM_198277 | SLC37A2 | 972 | 990 | U | U | C | C | U | c | U | A | C | U | G | G | C | U | G | C | c | c | c | 5 | 4 | 10 | c | false | <90% | 2720 | ||
| NM_144721 | THAP6 | 2832 | 2850 | g | c | a | C | U | c | U | A | C | U | G | G | C | U | G | C | U | U | A | 3 | 4 | 13 | bc | false | <90% | 3578 | ||
| NM_138348 | FAM105B | 1633 | 1651 | U | U | C | C | U | A | U | A | C | a | G | u | C | U | G | C | U | U | u | -21 | 3 | 9 | false | <90% | 7896 | |||
| XM_001132317 | LOC401397 | 147 | 165 | U | U | C | C | U | g | U | A | a | U | G | G | C | U | G | C | U | U | c | -28 | 3 | 9 | bc | false | <90% | 1151 | ||
| XM_001127122 | LOC401397 | 147 | 165 | U | U | C | C | U | g | U | A | a | U | G | G | C | U | G | C | U | U | c | -28 | 3 | 9 | bc | false | <90% | 1151 | ||
| XM_001127063 | LOC401397 | 147 | 165 | U | U | C | C | U | g | U | A | a | U | G | G | C | U | G | C | U | U | c | -28 | 3 | 9 | bc | false | <90% | 1151 | ||
| NM_001005200 | OR8H2 | 276 | 294 | U | U | C | C | U | u | U | A | C | g | G | G | C | U | G | C | U | U | u | -51 | 3 | 8 | bc | false | <90% | 939 | ||
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 | |||||||||||||
| XM_001130839 | NR1D2 | 4153 | 4171 | a | A | A | G | C | A | G | C | C | A | a | U | u | U | A | G | G | A | A | 26 | 3 | 9 | false | <90% | 5217 | |||
| NM_152388 | ALS2CR4 | 2564 | 2582 | U | A | A | G | C | u | G | g | C | A | G | U | A | U | A | G | G | A | g | -30 | 3 | 10 | bc | false | <90% | 5335 | ||
| NM_001044385 | ALS2CR4 | 2628 | 2646 | U | A | A | G | C | u | G | g | C | A | G | U | A | U | A | G | G | A | g | -30 | 3 | 10 | bc | false | <90% | 5399 | ||
3 prime UTR Seed matches
Hits to same gene : 0
Hits to other genes : 2412
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