Automatic recommendation
OK - siRNA is specific for both sense and antisense (guide) strands
22 hits were found for AGGCCUUGUGGUACUGCCU (10 guide strand hits and 12 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_025155 | WDR71 | 469 | 487 | A | G | G | C | C | U | U | G | U | G | G | U | c | C | U | G | a | g | U | 63 | 3 | 12 | false | <90% | 1585 | |||
NM_207128 | PAOX | 1175 | 1193 | u | G | G | C | u | U | U | G | U | G | G | U | c | C | U | G | C | C | U | 36 | 3 | 7 | false | <90% | 1720 | |||
NM_152911 | PAOX | 1175 | 1193 | u | G | G | C | u | U | U | G | U | G | G | U | c | C | U | G | C | C | U | 36 | 3 | 7 | false | <90% | 1878 | |||
NM_013974 | DDAH2 | 1140 | 1158 | u | G | G | C | C | U | U | G | g | G | G | U | A | C | U | G | C | u | g | 30 | 4 | 8 | c | false | <90% | 1351 | ||
NM_172369 | C1QC | 1048 | 1066 | A | u | G | C | C | U | U | c | U | G | G | U | A | C | U | G | C | C | a | 21 | 3 | 10 | bc | false | <90% | 1171 | ||
NM_001543 | NDST1 | 3676 | 3694 | g | G | G | C | C | U | U | G | g | G | G | c | A | C | U | G | C | C | U | 4 | 3 | 7 | false | <90% | 7913 | |||
NM_001079871 | HAP1 | 2238 | 2256 | A | G | G | C | C | U | U | c | U | G | G | g | A | C | U | G | C | C | c | 0 | 3 | 7 | false | <90% | 3869 | |||
NM_001079870 | HAP1 | 2262 | 2280 | A | G | G | C | C | U | U | c | U | G | G | g | A | C | U | G | C | C | c | 0 | 3 | 7 | false | <90% | 3893 | |||
NM_177977 | HAP1 | 2313 | 2331 | A | G | G | C | C | U | U | c | U | G | G | g | A | C | U | G | C | C | c | 0 | 3 | 7 | false | <90% | 3944 | |||
NM_003949 | HAP1 | 2469 | 2487 | A | G | G | C | C | U | U | c | U | G | G | g | A | C | U | G | C | C | c | 0 | 3 | 7 | false | <90% | 4100 |
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_379904 | MUC12 | 1006 | 1024 | c | G | G | C | A | G | U | A | C | C | A | C | A | A | c | G | C | C | a | 68 | 3 | 13 | c | false | <90% | 5184 | ||
XM_379904 | MUC12 | 3080 | 3098 | c | G | G | C | A | G | U | A | C | C | A | C | A | A | c | G | C | C | a | 68 | 3 | 13 | c | false | <90% | 5184 | ||
NM_032645 | RAPSN | 836 | 854 | A | G | c | C | A | G | U | A | C | C | A | C | A | u | G | G | C | C | g | 55 | 3 | 10 | c | false | <90% | 1541 | ||
NM_005055 | RAPSN | 836 | 854 | A | G | c | C | A | G | U | A | C | C | A | C | A | u | G | G | C | C | g | 55 | 3 | 10 | c | false | <90% | 1664 | ||
NM_020170 | NCLN | 439 | 457 | g | a | G | C | A | G | U | A | C | C | A | g | A | A | G | G | C | C | c | 47 | 4 | 9 | false | <90% | 3749 | |||
NM_000283 | PDE6B | 807 | 825 | A | G | G | C | A | G | U | u | C | C | A | C | A | A | G | G | C | C | U | 37 | 1 | 11 | bc | false | <90% | 3283 | ||
NM_178468 | FAM83C | 1910 | 1928 | A | u | G | C | A | G | U | A | C | C | c | C | A | A | G | G | C | C | c | 22 | 3 | 8 | c | false | <90% | 3188 | ||
NM_198889 | ANKRD17 | 324 | 342 | c | a | G | C | A | G | c | A | C | C | A | C | A | A | G | G | C | C | a | 15 | 4 | 11 | bc | false | <90% | 8637 | ||
NM_032217 | ANKRD17 | 324 | 342 | c | a | G | C | A | G | c | A | C | C | A | C | A | A | G | G | C | C | a | 15 | 4 | 11 | bc | false | <90% | 9390 | ||
NM_194302 | CCDC108 | 4670 | 4688 | A | G | G | C | A | G | U | A | u | C | A | C | A | A | G | G | a | g | c | 8 | 4 | 8 | c | false | <90% | 5975 | ||
NM_133499 | SYN1 | 1089 | 1107 | g | G | G | C | A | G | a | A | C | u | A | C | A | A | G | G | C | C | U | -51 | 3 | 9 | bc | false | <90% | 3172 | ||
NM_006950 | SYN1 | 1089 | 1107 | g | G | G | C | A | G | a | A | C | u | A | C | A | A | G | G | C | C | U | -51 | 3 | 9 | bc | false | <90% | 3210 |
3 prime UTR Seed matches
Hits to same gene : 0
Hits to other genes : 2365
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