Automatic recommendation
Warning - siRNA is specific for only the antisense (guide) strand
23 hits were found for UUGGAAAGGGGAGCAUUGA (14 guide strand hits and 9 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_004097 | EMX1 | 2013 | 2031 | g | a | G | G | A | A | A | G | G | G | G | A | G | g | A | U | U | G | g | 62 | 4 | 11 | c | false | <90% | 2188 | ||
NM_001040404 | EMX1 | 2047 | 2065 | g | a | G | G | A | A | A | G | G | G | G | A | G | g | A | U | U | G | g | 62 | 4 | 11 | c | false | <90% | 2222 | ||
NM_004711 | SYNGR1 | 1100 | 1118 | c | U | G | G | A | A | A | G | G | G | G | A | G | C | g | a | U | G | A | 47 | 3 | 13 | c | false | <90% | 4425 | ||
NM_181783 | TMTC3 | 860 | 878 | g | U | G | G | A | A | A | G | G | G | u | A | G | C | A | U | U | c | c | 29 | 4 | 9 | c | false | <90% | 4997 | ||
XR_016061 | LOC732173 | 419 | 437 | U | g | G | G | A | A | A | G | c | G | G | A | G | C | A | U | U | G | A | 28 | 2 | 10 | bc | false | <90% | 1838 | ||
NM_018996 | TNRC6C | 5066 | 5084 | g | U | G | G | c | A | A | G | G | G | G | A | G | C | A | g | U | G | A | 20 | 3 | 10 | c | false | <90% | 5318 | ||
NM_003583 | DYRK2 | 694 | 712 | U | U | G | G | g | A | A | G | G | G | G | A | G | C | u | U | U | G | g | 18 | 3 | 9 | c | false | <90% | 3466 | ||
NM_006482 | DYRK2 | 843 | 861 | U | U | G | G | g | A | A | G | G | G | G | A | G | C | u | U | U | G | g | 18 | 3 | 9 | c | false | <90% | 3615 | ||
NM_194435 | VIP | 624 | 642 | a | U | G | G | A | A | A | G | a | G | G | A | G | C | A | g | U | G | A | 11 | 3 | 7 | c | false | <90% | 1615 | ||
NM_003381 | VIP | 627 | 645 | a | U | G | G | A | A | A | G | a | G | G | A | G | C | A | g | U | G | A | 11 | 3 | 7 | c | false | <90% | 1618 | ||
NM_003943 | GENX-3414 | 877 | 895 | a | U | G | G | A | A | A | G | G | G | u | A | G | C | A | g | U | G | A | 10 | 3 | 9 | c | false | <90% | 2339 | ||
NM_147202 | C9orf25 | 2690 | 2708 | c | U | G | G | A | A | u | G | G | G | G | A | G | C | A | a | U | G | A | 5 | 3 | 8 | c | false | <90% | 3641 | ||
XM_941485 | LOC652147 | 1598 | 1616 | c | U | G | u | A | A | A | G | G | a | G | A | G | C | A | U | U | G | A | -21 | 3 | 9 | bc | false | <90% | 4869 | ||
NM_014014 | ASCC3L1 | 3226 | 3244 | c | U | G | u | A | A | A | G | G | a | G | A | G | C | A | U | U | G | A | -21 | 3 | 9 | bc | false | <90% | 7184 |
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_145693 | LPIN1 | 197 | 215 | c | C | A | A | U | G | C | U | C | C | C | C | U | U | U | C | C | A | c | 93 | 2 | 17 | abc | false | <90% | 5363 | ||
XM_001128450 | LOC728229 | 2523 | 2541 | U | C | A | A | U | G | C | U | C | C | C | C | U | U | U | C | C | u | u | 92 | 2 | 17 | ac | false | <90% | 2916 | ||
XM_001131298 | LOC730990 | 2526 | 2544 | U | C | A | A | U | G | C | U | C | C | C | C | U | U | U | C | C | u | u | 92 | 2 | 17 | ac | false | <90% | 2919 | ||
XM_001128423 | LOC728229 | 2553 | 2571 | U | C | A | A | U | G | C | U | C | C | C | C | U | U | U | C | C | u | u | 92 | 2 | 17 | ac | false | <90% | 2946 | ||
XM_928466 | LOC645426 | 2556 | 2574 | U | C | A | A | U | G | C | U | C | C | C | C | U | U | U | C | C | u | u | 92 | 2 | 17 | ac | false | <90% | 2949 | ||
NM_014690 | FAM131B | 673 | 691 | U | C | A | A | U | G | C | U | C | C | C | C | U | U | c | C | C | A | A | 75 | 1 | 14 | c | false | <90% | 5859 | ||
NM_024420 | PLA2G4A | 2007 | 2025 | a | a | c | A | a | G | C | U | C | C | C | C | U | U | U | C | C | A | A | 15 | 4 | 14 | bc | false | <90% | 2940 | ||
NM_144595 | SLAIN1 | 605 | 623 | a | a | g | A | U | G | u | U | C | C | C | C | U | U | U | C | C | A | A | 0 | 4 | 12 | bc | false | <90% | 2310 | ||
NM_001040153 | SLAIN1 | 669 | 687 | a | a | g | A | U | G | u | U | C | C | C | C | U | U | U | C | C | A | A | 0 | 4 | 12 | bc | false | <90% | 2374 |
3 prime UTR Seed matches
Hits to same gene : 0
Hits to other genes : 4648
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