Automatic recommendation
OK - siRNA is specific for both sense and antisense (guide) strands
16 hits were found for UCUCCGCGAGGACUGGGGA (5 guide strand hits and 11 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 | |||||||||||||
XM_939240 | LOC389813 | 1995 | 2013 | c | C | g | C | C | G | C | G | A | G | G | A | C | U | G | G | G | a | c | 70 | 4 | 14 | c | false | <90% | 2832 | ||
NM_001080482 | LOC389813 | 1995 | 2013 | c | C | g | C | C | G | C | G | A | G | G | A | C | U | G | G | G | a | c | 70 | 4 | 14 | c | false | <90% | 2832 | ||
NM_152856 | RBM10 | 2315 | 2333 | c | C | U | C | C | G | C | G | A | G | G | A | C | U | G | G | u | G | g | 69 | 3 | 15 | ac | false | <90% | 3190 | ||
NM_005676 | RBM10 | 2549 | 2567 | c | C | U | C | C | G | C | G | A | G | G | A | C | U | G | G | u | G | g | 69 | 3 | 15 | ac | false | <90% | 3415 | ||
NM_031917 | ANGPTL6 | 1233 | 1251 | U | C | U | C | C | u | g | G | A | G | G | A | C | U | G | G | G | G | g | -34 | 3 | 11 | bc | false | <90% | 1857 |
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_001037343 | CDKL5 | 1668 | 1686 | U | C | C | C | C | A | G | U | C | C | U | C | u | a | G | G | A | G | u | 65 | 3 | 12 | false | <90% | 3430 | |||
NM_003159 | CDKL5 | 1672 | 1690 | U | C | C | C | C | A | G | U | C | C | U | C | u | a | G | G | A | G | u | 65 | 3 | 12 | false | <90% | 3434 | |||
NM_015432 | PLEKHG4 | 1178 | 1196 | U | C | C | C | C | A | G | U | C | C | U | C | a | C | G | G | c | a | A | 63 | 3 | 12 | false | <90% | 6826 | |||
NM_182539 | MGC33600 | 1043 | 1061 | c | a | C | C | C | A | G | U | C | C | U | C | G | a | G | G | A | G | c | 62 | 4 | 11 | c | false | <90% | 1662 | ||
NM_001079804 | GAA | 239 | 257 | U | C | C | C | C | A | G | U | C | C | U | g | G | a | G | G | A | G | A | 46 | 2 | 11 | false | <90% | 3517 | |||
NM_001079803 | GAA | 319 | 337 | U | C | C | C | C | A | G | U | C | C | U | g | G | a | G | G | A | G | A | 46 | 2 | 11 | false | <90% | 3597 | |||
NM_000152 | GAA | 504 | 522 | U | C | C | C | C | A | G | U | C | C | U | g | G | a | G | G | A | G | A | 46 | 2 | 11 | false | <90% | 3782 | |||
XM_944606 | LOC646482 | 688 | 706 | g | C | C | C | C | A | G | g | C | C | U | C | G | C | G | G | A | G | c | 30 | 3 | 10 | bc | false | <90% | 1674 | ||
XM_933644 | LOC646482 | 688 | 706 | g | C | C | C | C | A | G | g | C | C | U | C | G | C | G | G | A | G | c | 30 | 3 | 10 | bc | false | <90% | 1674 | ||
XM_944973 | LOC651842 | 692 | 710 | g | C | C | C | C | A | G | g | C | C | U | C | G | C | G | G | A | a | c | 28 | 4 | 9 | c | false | <90% | 960 | ||
XM_931742 | LOC643678 | 692 | 710 | g | C | C | C | C | A | G | g | C | C | U | C | G | C | G | G | A | a | c | 28 | 4 | 9 | c | false | <90% | 960 |
3 prime UTR Seed matches
Hits to same gene : 0
Hits to other genes : 577
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