Automatic recommendation
OK - siRNA is specific for both sense and antisense (guide) strands
7 hits were found for GCUCAUCGGAACUGACAAU (5 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_004615 | TSPAN7 | 244 | 262 | G | C | U | C | A | U | C | G | G | A | A | C | U | G | g | C | A | c | c | 67 | 3 | 14 | c | false | <90% | 1813 | ||
NM_032281 | ELAVL3 | 3221 | 3239 | c | C | c | C | A | U | C | G | G | A | A | C | U | G | A | g | A | A | U | 52 | 3 | 12 | c | false | <90% | 4661 | ||
NM_001420 | ELAVL3 | 3242 | 3260 | c | C | c | C | A | U | C | G | G | A | A | C | U | G | A | g | A | A | U | 52 | 3 | 12 | c | false | <90% | 4682 | ||
NM_032221 | CHD6 | 4930 | 4948 | G | C | U | C | A | U | C | G | G | c | A | C | U | G | c | C | A | A | a | -12 | 3 | 9 | c | false | <90% | 10389 | ||
NM_207517 | ADAMTSL3 | 3206 | 3224 | G | C | U | C | A | U | u | G | G | u | A | C | U | G | A | C | A | A | c | -54 | 3 | 8 | bc | false | <90% | 7336 |
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_000570 | FCGR3B | 2109 | 2127 | c | a | U | G | U | C | A | G | U | U | C | C | a | A | U | G | A | G | g | 71 | 4 | 10 | false | <90% | 2300 | |||
NM_000569 | FCGR3A | 2124 | 2142 | c | a | U | G | U | C | A | G | U | U | C | C | a | A | U | G | A | G | g | 71 | 4 | 10 | false | <90% | 2406 |
3 prime UTR Seed matches
Hits to same gene : 0
Hits to other genes : 1258
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