Automatic recommendation
OK - siRNA is specific for both sense and antisense (guide) strands
35 hits were found for CUGUGACAUUGGAGAGUCA (12 guide strand hits and 23 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_016610 | TLR8 | 2536 | 2554 | C | U | G | U | G | A | C | A | U | U | G | G | A | G | A | u | U | u | c | 66 | 3 | 15 | c | false | <90% | 3468 | ||
NM_138636 | TLR8 | 2399 | 2417 | C | U | G | U | G | A | C | A | U | U | G | G | A | G | A | u | U | u | c | 66 | 3 | 15 | c | false | <90% | 4211 | ||
NM_002111 | HD | 2152 | 2170 | a | g | G | U | G | A | C | A | U | U | G | G | A | c | A | G | U | C | c | 62 | 4 | 11 | c | false | <90% | 13481 | ||
NM_001080432 | FTO | 2727 | 2745 | u | g | a | U | G | A | C | A | U | U | G | G | A | G | A | c | U | C | A | 40 | 4 | 12 | c | false | <90% | 4294 | ||
XM_941142 | FTO | 2727 | 2745 | u | g | a | U | G | A | C | A | U | U | G | G | A | G | A | c | U | C | A | 40 | 4 | 12 | c | false | <90% | 4294 | ||
NM_016616 | TXNDC3 | 1230 | 1248 | C | U | G | U | G | A | C | A | U | U | G | a | A | G | A | G | g | a | u | 35 | 4 | 11 | false | <90% | 2350 | |||
NM_153280 | UBE1 | 687 | 705 | C | U | G | U | G | A | C | u | U | U | G | G | A | G | A | G | g | a | A | 11 | 3 | 8 | c | false | <90% | 3483 | ||
NM_003334 | UBE1 | 726 | 744 | C | U | G | U | G | A | C | u | U | U | G | G | A | G | A | G | g | a | A | 11 | 3 | 8 | c | false | <90% | 3504 | ||
XM_932109 | CEP78 | 1457 | 1475 | C | U | G | U | G | A | C | A | g | U | a | G | A | G | A | G | U | C | c | -26 | 3 | 8 | c | false | <90% | 2304 | ||
XM_943379 | CEP78 | 1457 | 1475 | C | U | G | U | G | A | C | A | g | U | a | G | A | G | A | G | U | C | c | -26 | 3 | 8 | c | false | <90% | 2304 | ||
NM_138732 | NRXN2 | 1827 | 1845 | C | U | G | U | G | A | C | c | U | U | u | G | A | G | A | G | U | C | c | -28 | 3 | 7 | c | false | <90% | 6390 | ||
NM_015080 | NRXN2 | 1920 | 1938 | C | U | G | U | G | A | C | c | U | U | u | G | A | G | A | G | U | C | c | -28 | 3 | 7 | c | false | <90% | 6616 |
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_000895 | LTA4H | 931 | 949 | U | c | A | C | U | C | U | C | C | A | A | U | G | U | C | A | u | u | G | 62 | 3 | 14 | ac | false | <90% | 2060 | ||
XM_001133842 | LOC729446 | 6669 | 6687 | U | G | A | C | U | C | U | C | C | A | g | U | G | U | C | A | C | g | a | 31 | 3 | 10 | c | false | <90% | 7377 | ||
NM_012115 | CASP8AP2 | 6286 | 6304 | U | G | A | C | U | C | U | C | u | A | A | U | u | U | C | A | C | A | u | 24 | 3 | 8 | false | <90% | 6782 | |||
XM_939510 | DUB3 | 594 | 612 | a | G | A | u | U | C | U | C | C | g | A | U | G | U | C | A | C | A | G | -21 | 3 | 9 | bc | false | <90% | 945 | ||
XM_939458 | LOC650373 | 321 | 339 | a | G | A | u | U | C | U | C | C | g | A | U | G | U | C | A | C | A | G | -21 | 3 | 9 | bc | false | <90% | 1068 | ||
XR_017907 | DUB4 | 846 | 864 | a | G | A | u | U | C | U | C | C | g | A | U | G | U | C | A | C | A | G | -21 | 3 | 9 | bc | false | <90% | 1197 | ||
XR_019571 | LOC652732 | 847 | 865 | a | G | A | u | U | C | U | C | C | g | A | U | G | U | C | A | C | A | G | -21 | 3 | 9 | bc | false | <90% | 1200 | ||
XR_018109 | LOC647334 | 847 | 865 | a | G | A | u | U | C | U | C | C | g | A | U | G | U | C | A | C | A | G | -21 | 3 | 9 | bc | false | <90% | 1200 | ||
XR_016895 | LOC402329 | 847 | 865 | a | G | A | u | U | C | U | C | C | g | A | U | G | U | C | A | C | A | G | -21 | 3 | 9 | bc | false | <90% | 1201 | ||
XR_016952 | LOC392187 | 847 | 865 | a | G | A | u | U | C | U | C | C | g | A | U | G | U | C | A | C | A | G | -21 | 3 | 9 | bc | false | <90% | 1201 | ||
NR_003275 | LOC392196 | 845 | 863 | a | G | A | u | U | C | U | C | C | g | A | U | G | U | C | A | C | A | G | -21 | 3 | 9 | bc | false | <90% | 1438 | ||
XM_373243 | LOC392197 | 846 | 864 | a | G | A | u | U | C | U | C | C | g | A | U | G | U | C | A | C | A | G | -21 | 3 | 9 | bc | false | <90% | 1593 | ||
XM_938441 | LOC649368 | 846 | 864 | a | G | A | u | U | C | U | C | C | g | A | U | G | U | C | A | C | A | G | -21 | 3 | 9 | bc | false | <90% | 1593 | ||
NM_201402 | DUB3 | 846 | 864 | a | G | A | u | U | C | U | C | C | g | A | U | G | U | C | A | C | A | G | -21 | 3 | 9 | bc | false | <90% | 1593 | ||
XM_001130410 | LOC728369 | 846 | 864 | a | G | A | u | U | C | U | C | C | g | A | U | G | U | C | A | C | A | G | -21 | 3 | 9 | bc | false | <90% | 1593 | ||
XM_001130417 | LOC728373 | 846 | 864 | a | G | A | u | U | C | U | C | C | g | A | U | G | U | C | A | C | A | G | -21 | 3 | 9 | bc | false | <90% | 1593 | ||
XM_001130428 | LOC728379 | 846 | 864 | a | G | A | u | U | C | U | C | C | g | A | U | G | U | C | A | C | A | G | -21 | 3 | 9 | bc | false | <90% | 1593 | ||
XM_001130437 | LOC728386 | 846 | 864 | a | G | A | u | U | C | U | C | C | g | A | U | G | U | C | A | C | A | G | -21 | 3 | 9 | bc | false | <90% | 1593 | ||
XM_001130444 | LOC728393 | 846 | 864 | a | G | A | u | U | C | U | C | C | g | A | U | G | U | C | A | C | A | G | -21 | 3 | 9 | bc | false | <90% | 1593 | ||
XM_001130452 | LOC728400 | 846 | 864 | a | G | A | u | U | C | U | C | C | g | A | U | G | U | C | A | C | A | G | -21 | 3 | 9 | bc | false | <90% | 1593 | ||
XM_001130464 | LOC728405 | 846 | 864 | a | G | A | u | U | C | U | C | C | g | A | U | G | U | C | A | C | A | G | -21 | 3 | 9 | bc | false | <90% | 1593 | ||
XM_001130476 | LOC728419 | 846 | 864 | a | G | A | u | U | C | U | C | C | g | A | U | G | U | C | A | C | A | G | -21 | 3 | 9 | bc | false | <90% | 1593 | ||
XM_376305 | DUB3 | 846 | 864 | a | G | A | u | U | C | U | C | C | g | A | U | G | U | C | A | C | A | G | -21 | 3 | 9 | bc | false | <90% | 1593 |
3 prime UTR Seed matches
Hits to same gene : 0
Hits to other genes : 2647
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