Automatic recommendation
OK - siRNA is specific for both sense and antisense (guide) strands
10 hits were found for CGGCUUCGCCGAGAUCAGA (7 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_016269 | LEF1 | 762 | 780 | g | a | u | C | U | U | C | G | C | C | G | A | G | A | U | C | A | G | u | 62 | 4 | 15 | bc | false | <90% | 3084 | ||
XM_941552 | LOC652189 | 753 | 771 | g | a | G | C | U | U | C | G | C | C | G | A | G | c | U | C | A | G | g | 62 | 4 | 11 | c | false | <90% | 1710 | ||
NM_001080460 | LOC344657 | 753 | 771 | g | a | G | C | U | U | C | G | C | C | G | A | G | c | U | C | A | G | g | 62 | 4 | 11 | c | false | <90% | 1825 | ||
XM_938665 | USP6NL | 171 | 189 | C | G | G | C | U | U | C | G | C | C | G | g | G | A | U | C | c | u | c | 35 | 4 | 11 | false | <90% | 4829 | |||
XM_927409 | USP6NL | 171 | 189 | C | G | G | C | U | U | C | G | C | C | G | g | G | A | U | C | c | u | c | 35 | 4 | 11 | false | <90% | 4829 | |||
NM_013286 | RBM15B | 592 | 610 | g | c | G | C | U | U | C | G | g | C | G | A | G | A | U | C | A | G | c | 21 | 4 | 9 | bc | false | <90% | 6620 | ||
NM_002518 | NPAS2 | 1605 | 1623 | C | G | G | C | U | U | u | G | C | C | a | A | G | A | U | C | A | G | c | -32 | 3 | 7 | c | false | <90% | 4004 |
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 | |||||||||||||
XR_017778 | LOC439951 | 729 | 747 | g | a | g | G | A | U | C | c | C | G | G | C | G | A | A | G | C | C | G | 4 | 4 | 11 | bc | false | <90% | 1370 | ||
XR_017773 | LOC439951 | 729 | 747 | g | a | g | G | A | U | C | c | C | G | G | C | G | A | A | G | C | C | G | 4 | 4 | 11 | bc | false | <90% | 1370 | ||
NR_003047 | SNORD19 | 49 | 67 | U | C | U | G | A | U | C | U | C | a | G | C | a | A | A | G | C | C | x | 1 | 3 | 9 | false | <90% | 76 |
3 prime UTR Seed matches
Hits to same gene : 0
Hits to other genes : 659
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