Automatic recommendation
OK - siRNA is specific for both sense and antisense (guide) strands
14 hits were found for UUAAUAGACAAUGACCACA (12 guide strand hits and 2 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_145753 | PHLDB2 | 998 | 1016 | g | U | A | A | U | A | G | A | C | A | A | U | G | A | C | a | A | u | u | 64 | 4 | 14 | c | false | <90% | 5491 | ||
| NM_003841 | TNFRSF10C | 783 | 801 | U | g | A | A | g | A | G | A | C | A | A | U | G | A | C | C | A | C | c | 32 | 3 | 13 | bc | false | <90% | 1404 | ||
| NM_003841 | TNFRSF10C | 828 | 846 | U | g | A | A | g | A | G | A | C | A | A | U | G | A | C | C | A | C | c | 32 | 3 | 13 | bc | false | <90% | 1404 | ||
| NM_003841 | TNFRSF10C | 873 | 891 | U | g | A | A | g | A | G | A | C | A | A | U | G | A | C | C | A | C | c | 32 | 3 | 13 | bc | false | <90% | 1404 | ||
| XR_017556 | LOC391578 | 2045 | 2063 | g | U | c | A | U | A | G | A | a | A | A | U | G | A | C | C | A | C | A | 18 | 3 | 10 | bc | false | <90% | 3984 | ||
| XR_019645 | LOC391578 | 2045 | 2063 | g | U | c | A | U | A | G | A | a | A | A | U | G | A | C | C | A | C | A | 18 | 3 | 10 | bc | false | <90% | 3984 | ||
| NM_004117 | FKBP5 | 144 | 162 | U | U | A | A | a | A | G | A | C | A | A | U | G | A | C | u | A | C | u | 17 | 3 | 10 | c | false | <90% | 3781 | ||
| NM_080739 | C20orf141 | 701 | 719 | c | a | A | A | U | A | u | A | C | A | A | U | G | A | C | C | A | C | c | 15 | 4 | 11 | bc | false | <90% | 741 | ||
| NM_015192 | PLCB1 | 4731 | 4749 | U | U | A | A | U | u | G | A | C | A | A | U | G | A | C | C | c | a | A | 10 | 3 | 10 | c | false | <90% | 6705 | ||
| NM_182734 | PLCB1 | 4849 | 4867 | U | U | A | A | U | u | G | A | C | A | A | U | G | A | C | C | c | a | A | 10 | 3 | 10 | c | false | <90% | 6823 | ||
| NM_005971 | FXYD3 | 1097 | 1115 | a | U | A | A | c | A | u | A | C | A | A | U | G | A | C | C | A | C | A | -19 | 3 | 12 | bc | false | <90% | 1304 | ||
| NM_021910 | FXYD3 | 1259 | 1277 | a | U | A | A | c | A | u | A | C | A | A | U | G | A | C | C | A | C | A | -19 | 3 | 12 | bc | false | <90% | 1466 | ||
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_012351 | OR10J1 | 768 | 786 | U | G | U | G | G | U | C | A | U | U | G | U | C | c | A | c | U | A | c | 49 | 3 | 13 | c | false | <90% | 963 | ||
| NM_001557 | IL8RB | 556 | 574 | U | G | U | G | G | U | C | A | U | U | a | U | C | U | A | U | g | c | c | 7 | 4 | 10 | c | false | <90% | 2859 | ||
3 prime UTR Seed matches
Hits to same gene : 0
Hits to other genes : 2089
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