Automatic recommendation
OK - siRNA is specific for both sense and antisense (guide) strands
18 hits were found for GGCCUUGUGGUACUGCCUG (6 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_207128 | PAOX | 1176 | 1194 | G | G | C | u | U | U | G | U | G | G | U | c | C | U | G | C | C | U | G | 29 | 2 | 7 | false | <90% | 1720 | |||
NM_152911 | PAOX | 1176 | 1194 | G | G | C | u | U | U | G | U | G | G | U | c | C | U | G | C | C | U | G | 29 | 2 | 7 | false | <90% | 1878 | |||
NM_172369 | C1QC | 1049 | 1067 | u | G | C | C | U | U | c | U | G | G | U | A | C | U | G | C | C | a | u | 24 | 4 | 10 | c | false | <90% | 1171 | ||
NM_013974 | DDAH2 | 1141 | 1159 | G | G | C | C | U | U | G | g | G | G | U | A | C | U | G | C | u | g | G | 11 | 3 | 8 | c | false | <90% | 1351 | ||
NM_144707 | PROM2 | 2470 | 2488 | u | G | C | C | U | U | c | U | G | G | U | u | C | U | G | C | C | U | G | -2 | 3 | 7 | false | <90% | 3822 | |||
NM_001543 | NDST1 | 3677 | 3695 | G | G | C | C | U | U | G | g | G | G | c | A | C | U | G | C | C | U | u | -28 | 3 | 7 | c | false | <90% | 7913 |
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 | 1005 | 1023 | C | c | G | G | C | A | G | U | A | C | C | A | C | A | A | c | G | C | C | 62 | 2 | 13 | c | false | <90% | 5184 | ||
XM_379904 | MUC12 | 3079 | 3097 | C | c | G | G | C | A | G | U | A | C | C | A | C | A | A | c | G | C | C | 62 | 2 | 13 | c | false | <90% | 5184 | ||
NM_020170 | NCLN | 440 | 458 | C | g | a | G | C | A | G | U | A | C | C | A | g | A | A | G | G | C | C | 58 | 3 | 9 | false | <90% | 3749 | |||
NM_178468 | FAM83C | 1911 | 1929 | g | A | u | G | C | A | G | U | A | C | C | c | C | A | A | G | G | C | C | 44 | 3 | 8 | false | <90% | 3188 | |||
NM_000283 | PDE6B | 807 | 825 | g | A | G | G | C | A | G | U | u | C | C | A | C | A | A | G | G | C | C | 37 | 2 | 10 | bc | false | <90% | 3283 | ||
NM_032645 | RAPSN | 837 | 855 | g | A | G | c | C | A | G | U | A | C | C | A | C | A | u | G | G | C | C | 36 | 3 | 10 | c | false | <90% | 1541 | ||
NM_005055 | RAPSN | 837 | 855 | g | A | G | c | C | A | G | U | A | C | C | A | C | A | u | G | G | C | C | 36 | 3 | 10 | c | false | <90% | 1664 | ||
NM_000448 | RAG1 | 1565 | 1583 | C | A | G | u | C | A | G | U | A | C | C | A | C | A | A | G | a | u | g | 32 | 4 | 12 | c | false | <90% | 6557 | ||
NM_014714 | IFT140 | 3302 | 3320 | C | A | u | G | C | u | G | U | A | C | C | A | C | A | A | G | G | C | u | 12 | 3 | 12 | bc | false | <90% | 4966 | ||
NM_194302 | CCDC108 | 4671 | 4689 | g | A | G | G | C | A | G | U | A | u | C | A | C | A | A | G | G | a | g | 7 | 4 | 8 | c | false | <90% | 5975 | ||
NM_198889 | ANKRD17 | 325 | 343 | g | c | a | G | C | A | G | c | A | C | C | A | C | A | A | G | G | C | C | 4 | 4 | 11 | bc | false | <90% | 8637 | ||
NM_032217 | ANKRD17 | 325 | 343 | g | c | a | G | C | A | G | c | A | C | C | A | C | A | A | G | G | C | C | 4 | 4 | 11 | bc | false | <90% | 9390 |
3 prime UTR Seed matches
Hits to same gene : 0
Hits to other genes : 2442
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