Automatic recommendation
OK - siRNA is specific for both sense and antisense (guide) strands
20 hits were found for GGAUGAACAACUACAUGCA (17 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 | |||||||||||||
XM_001132171 | LOC730036 | 194 | 212 | c | a | A | U | G | A | A | C | A | A | C | U | A | C | A | U | G | u | u | 78 | 4 | 15 | ac | false | <90% | 2479 | ||
XM_001126197 | LOC730523 | 194 | 212 | c | a | A | U | G | A | A | C | A | A | C | U | A | C | A | U | G | u | u | 78 | 4 | 15 | ac | false | <90% | 2479 | ||
XR_016253 | LOC642907 | 314 | 332 | c | G | A | U | G | A | A | C | A | A | C | U | A | C | c | U | G | u | u | 65 | 4 | 13 | c | false | <90% | 874 | ||
XM_934286 | LOC647070 | 348 | 366 | u | u | A | U | G | A | A | C | A | A | C | U | A | u | A | U | G | C | c | 62 | 4 | 11 | c | false | <90% | 1019 | ||
XM_944562 | LOC647070 | 348 | 366 | u | u | A | U | G | A | A | C | A | A | C | U | A | u | A | U | G | C | c | 62 | 4 | 11 | c | false | <90% | 1019 | ||
NM_014905 | GLS | 2681 | 2699 | G | u | u | U | G | A | A | C | A | A | C | U | A | u | A | U | G | C | A | 49 | 3 | 10 | c | false | <90% | 4799 | ||
NM_080684 | PTPN13 | 3074 | 3092 | a | G | A | U | G | A | A | a | A | A | C | U | A | C | A | U | G | a | A | 33 | 3 | 9 | c | false | <90% | 7546 | ||
NM_006264 | PTPN13 | 3590 | 3608 | a | G | A | U | G | A | A | a | A | A | C | U | A | C | A | U | G | a | A | 33 | 3 | 9 | c | false | <90% | 8062 | ||
NM_080683 | PTPN13 | 3647 | 3665 | a | G | A | U | G | A | A | a | A | A | C | U | A | C | A | U | G | a | A | 33 | 3 | 9 | c | false | <90% | 8119 | ||
NM_080685 | PTPN13 | 3647 | 3665 | a | G | A | U | G | A | A | a | A | A | C | U | A | C | A | U | G | a | A | 33 | 3 | 9 | c | false | <90% | 8133 | ||
NM_016388 | TRAT1 | 552 | 570 | a | G | A | U | G | A | g | C | A | A | C | U | A | C | A | U | G | C | A | 31 | 2 | 12 | bc | false | <90% | 1695 | ||
NM_004438 | EPHA4 | 4526 | 4544 | a | G | A | U | G | A | A | g | A | A | C | U | A | C | A | U | G | a | u | 28 | 4 | 9 | c | false | <90% | 6364 | ||
NM_003922 | HERC1 | 14670 | 14688 | a | c | A | U | G | g | A | C | A | A | C | U | A | C | A | U | G | C | u | 18 | 4 | 12 | bc | false | <90% | 15216 | ||
NM_145174 | DNAJB7 | 671 | 689 | G | G | A | U | G | g | A | C | A | A | C | U | A | C | A | U | a | u | c | 5 | 4 | 10 | c | false | <90% | 2578 | ||
NM_175856 | CHSY-2 | 722 | 740 | u | G | A | U | G | A | u | C | A | A | g | U | A | C | A | U | G | C | A | -29 | 3 | 8 | c | false | <90% | 3523 | ||
NR_003199 | SNORD114-7 | 41 | 59 | u | G | A | U | G | A | A | u | A | A | a | U | A | C | A | U | G | C | c | -30 | 4 | 7 | c | false | <90% | 76 | ||
NM_024552 | LASS4 | 1029 | 1047 | a | G | A | U | G | g | u | C | A | A | C | U | A | C | A | U | G | C | A | -31 | 3 | 12 | bc | false | <90% | 1774 |
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_020987 | ANK3 | 8804 | 8822 | c | G | C | A | U | G | U | A | c | U | U | G | U | U | C | A | U | g | a | 30 | 4 | 8 | c | false | <90% | 14771 | ||
NM_014747 | RIMS3 | 2459 | 2477 | U | G | C | A | U | G | a | A | G | U | U | G | U | U | C | A | U | u | u | 26 | 3 | 10 | c | false | <90% | 7233 | ||
NM_017637 | BNC2 | 6953 | 6971 | g | u | g | A | U | G | U | A | G | a | U | G | U | U | C | A | U | C | C | -15 | 4 | 9 | bc | false | <90% | 12926 |
3 prime UTR Seed matches
Hits to same gene : 0
Hits to other genes : 1954
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