Automatic recommendation
OK - siRNA is specific for both sense and antisense (guide) strands
10 hits were found for UUACUCGCUGAAGCUGGUA (4 guide strand hits and 6 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_001941 | DSC3 | 3663 | 3681 | a | U | A | C | U | C | G | C | U | G | c | A | G | C | U | G | G | g | g | 29 | 4 | 9 | c | false | <90% | 5879 | ||
NM_024423 | DSC3 | 3706 | 3724 | a | U | A | C | U | C | G | C | U | G | c | A | G | C | U | G | G | g | g | 29 | 4 | 9 | c | false | <90% | 5920 | ||
NM_000068 | CACNA1A | 6696 | 6714 | U | U | A | C | U | C | G | C | U | G | g | A | G | C | g | G | G | U | c | 9 | 3 | 10 | c | false | <90% | 7807 | ||
NM_023035 | CACNA1A | 6696 | 6714 | U | U | A | C | U | C | G | C | U | G | g | A | G | C | g | G | G | U | c | 9 | 3 | 10 | c | false | <90% | 7812 |
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_943661 | LRRC38 | 925 | 943 | g | g | C | C | A | G | C | U | U | C | A | G | C | G | A | G | U | g | u | 78 | 4 | 15 | ac | false | <90% | 2235 | ||
XM_059074 | LRRC38 | 970 | 988 | g | g | C | C | A | G | C | U | U | C | A | G | C | G | A | G | U | g | u | 78 | 4 | 15 | ac | false | <90% | 2280 | ||
NM_002357 | MXD1 | 617 | 635 | g | A | C | C | A | G | C | U | U | C | A | G | C | G | A | G | a | g | c | 66 | 4 | 15 | ac | false | <90% | 5587 | ||
XM_001129494 | LOC729152 | 249 | 267 | U | A | C | C | A | G | C | U | U | C | A | G | a | G | A | G | g | c | c | 58 | 4 | 12 | false | <90% | 891 | |||
NM_015490 | SEC31B | 3562 | 3580 | U | A | g | C | A | G | C | U | U | C | A | G | C | G | A | G | g | u | g | 49 | 4 | 13 | c | false | <90% | 4631 | ||
NM_003635 | NDST2 | 2692 | 2710 | U | A | C | C | A | G | C | a | U | C | A | G | C | G | A | G | c | c | c | 6 | 4 | 8 | c | false | <90% | 3778 |
3 prime UTR Seed matches
Hits to same gene : 0
Hits to other genes : 0
View matched accessions
3 prime seed match details
Accession | Gene name | Hits to this gene |
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