Automatic recommendation
Warning - siRNA is specific for only the antisense (guide) strand
24 hits were found for GUUUGGAAAGGGGAGCAUU (4 guide strand hits and 20 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_181783 | TMTC3 | 858 | 876 | c | c | g | U | G | G | A | A | A | G | G | G | u | A | G | C | A | U | U | 56 | 4 | 9 | false | <90% | 4997 | |||
XM_944015 | LOC388002 | 67 | 85 | G | U | U | g | G | G | A | A | A | G | G | G | G | A | G | C | u | c | a | 32 | 4 | 12 | c | false | <90% | 637 | ||
XM_373600 | LOC388002 | 67 | 85 | G | U | U | g | G | G | A | A | A | G | G | G | G | A | G | C | u | c | a | 32 | 4 | 12 | c | false | <90% | 637 | ||
XM_001129325 | LOC731354 | 143 | 161 | a | U | U | U | G | G | A | A | A | u | G | G | G | A | G | C | A | c | a | 7 | 4 | 8 | c | false | <90% | 423 |
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_014690 | FAM131B | 674 | 692 | A | A | U | G | C | U | C | C | C | C | U | U | c | C | C | A | A | A | a | 84 | 2 | 12 | false | <90% | 5859 | |||
NM_024420 | PLA2G4A | 2006 | 2024 | c | A | a | G | C | U | C | C | C | C | U | U | U | C | C | A | A | A | g | 73 | 3 | 15 | bc | false | <90% | 2940 | ||
NM_145693 | LPIN1 | 196 | 214 | A | A | U | G | C | U | C | C | C | C | U | U | U | C | C | A | c | g | u | 68 | 3 | 16 | ac | false | <90% | 5363 | ||
NM_020796 | SEMA6A | 3757 | 3775 | u | u | U | G | C | U | C | C | C | C | U | U | U | C | C | A | c | A | u | 58 | 4 | 14 | ac | false | <90% | 6860 | ||
XM_001128450 | LOC728229 | 2523 | 2541 | A | A | U | G | C | U | C | C | C | C | U | U | U | C | C | u | u | c | u | 42 | 4 | 15 | c | false | <90% | 2916 | ||
XM_001131298 | LOC730990 | 2526 | 2544 | A | A | U | G | C | U | C | C | C | C | U | U | U | C | C | u | u | c | u | 42 | 4 | 15 | c | false | <90% | 2919 | ||
XM_001128423 | LOC728229 | 2553 | 2571 | A | A | U | G | C | U | C | C | C | C | U | U | U | C | C | u | u | c | u | 42 | 4 | 15 | c | false | <90% | 2946 | ||
XM_928466 | LOC645426 | 2556 | 2574 | A | A | U | G | C | U | C | C | C | C | U | U | U | C | C | u | u | c | u | 42 | 4 | 15 | c | false | <90% | 2949 | ||
NM_144595 | SLAIN1 | 604 | 622 | g | A | U | G | u | U | C | C | C | C | U | U | U | C | C | A | A | A | g | 41 | 3 | 13 | bc | false | <90% | 2310 | ||
NM_001040153 | SLAIN1 | 668 | 686 | g | A | U | G | u | U | C | C | C | C | U | U | U | C | C | A | A | A | g | 41 | 3 | 13 | bc | false | <90% | 2374 | ||
NM_001077498 | C17orf63 | 2560 | 2578 | c | A | g | a | C | U | C | C | C | C | U | U | U | C | C | A | A | A | C | 41 | 3 | 15 | bc | false | <90% | 4163 | ||
NM_018182 | C17orf63 | 2594 | 2612 | c | A | g | a | C | U | C | C | C | C | U | U | U | C | C | A | A | A | C | 41 | 3 | 15 | bc | false | <90% | 4197 | ||
NM_003155 | STC1 | 624 | 642 | g | g | U | G | C | U | C | C | a | C | U | U | U | C | C | A | A | A | g | 21 | 4 | 9 | bc | false | <90% | 3897 | ||
NM_181337 | KAAG1 | 1283 | 1301 | u | g | U | G | C | U | a | C | C | C | U | U | U | C | C | A | A | A | C | 20 | 3 | 12 | bc | false | <90% | 1382 | ||
XM_937204 | LOC339742 | 131 | 149 | A | A | U | c | C | U | g | C | C | C | U | U | U | C | C | A | A | A | a | -8 | 3 | 11 | bc | false | <90% | 1443 | ||
XM_497879 | LOC442049 | 52 | 70 | A | A | U | c | C | U | g | C | C | C | U | U | U | C | C | A | A | A | a | -8 | 3 | 11 | bc | false | <90% | 1853 | ||
XR_016906 | LOC147711 | 107 | 125 | A | A | U | u | C | U | g | C | C | C | U | U | U | C | C | A | A | A | a | -8 | 3 | 11 | bc | false | <90% | 1969 | ||
XR_015733 | LOC732117 | 263 | 281 | A | A | U | u | C | U | g | C | C | C | U | U | U | C | C | A | A | A | a | -8 | 3 | 11 | bc | false | <90% | 2125 | ||
NM_152354 | ZNF285A | 59 | 77 | A | A | U | c | C | U | g | C | C | C | U | U | U | C | C | A | A | A | a | -8 | 3 | 11 | bc | false | <90% | 2703 | ||
XM_929878 | LOC646915 | 50 | 68 | A | A | U | c | C | U | g | C | C | C | U | U | U | C | C | A | A | A | a | -8 | 3 | 11 | bc | false | <90% | 2942 |
3 prime UTR Seed matches
Hits to same gene : 0
Hits to other genes : 2456
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