Automatic recommendation
OK - siRNA is specific for both sense and antisense (guide) strands
28 hits were found for CAGUCAUGAUGGUGGUUUA (15 guide strand hits and 13 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_024072 | DDX54 | 4071 | 4089 | C | A | G | U | g | A | U | G | A | U | G | G | U | G | G | U | U | c | c | 40 | 3 | 12 | c | false | <90% | 4401 | ||
XR_016373 | LOC642817 | 740 | 758 | C | A | G | c | C | A | U | G | A | U | G | G | U | G | G | U | g | g | A | 37 | 3 | 12 | c | false | <90% | 1348 | ||
XR_018564 | LOC642817 | 740 | 758 | C | A | G | c | C | A | U | G | A | U | G | G | U | G | G | U | g | g | A | 37 | 3 | 12 | c | false | <90% | 1349 | ||
XM_001129314 | LOC729099 | 420 | 438 | C | A | G | U | g | A | U | G | A | U | G | G | U | G | G | U | a | g | u | 17 | 4 | 11 | c | false | <90% | 615 | ||
XR_018923 | LOC648210 | 758 | 776 | C | A | G | U | C | A | U | G | g | U | G | G | U | G | G | U | g | g | A | 13 | 3 | 8 | c | false | <90% | 1753 | ||
XR_017337 | LOC644037 | 758 | 776 | C | A | G | U | C | A | U | G | g | U | G | G | U | G | G | U | g | g | A | 13 | 3 | 8 | c | false | <90% | 1753 | ||
NM_018151 | RIF1 | 2952 | 2970 | a | A | G | U | g | A | U | G | A | U | G | u | U | G | G | U | U | U | A | 12 | 3 | 7 | false | <90% | 8383 | |||
NM_024546 | C13orf7 | 2362 | 2380 | a | A | G | U | C | A | g | G | A | U | G | G | U | G | G | a | U | U | A | 5 | 3 | 8 | c | false | <90% | 3552 | ||
NM_003917 | AP1G2 | 330 | 348 | C | A | G | U | C | A | g | G | A | U | G | G | U | G | G | U | g | c | c | 2 | 4 | 9 | c | false | <90% | 2876 | ||
NM_080545 | AP1G2 | 753 | 771 | C | A | G | U | C | A | g | G | A | U | G | G | U | G | G | U | g | c | c | 2 | 4 | 9 | c | false | <90% | 3305 | ||
NM_000809 | GABRA4 | 3062 | 3080 | C | A | G | U | C | A | U | c | A | U | G | u | U | G | G | U | U | U | u | 0 | 3 | 7 | false | <90% | 11143 | |||
NM_194442 | LBR | 3422 | 3440 | C | A | G | U | C | A | U | G | A | a | G | u | U | G | G | U | U | U | g | -21 | 3 | 9 | false | <90% | 3789 | |||
NM_002296 | LBR | 3439 | 3457 | C | A | G | U | C | A | U | G | A | a | G | u | U | G | G | U | U | U | g | -21 | 3 | 9 | false | <90% | 3806 | |||
NM_016657 | KDELR3 | 338 | 356 | C | A | G | U | a | A | U | G | A | a | G | G | U | G | G | U | U | U | u | -39 | 3 | 8 | bc | false | <90% | 929 | ||
NM_006855 | KDELR3 | 338 | 356 | C | A | G | U | a | A | U | G | A | a | G | G | U | G | G | U | U | U | u | -39 | 3 | 8 | bc | false | <90% | 1705 |
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 | |||||||||||||
XR_017141 | LOC646289 | 126 | 144 | a | A | c | A | C | C | A | C | C | A | U | C | A | U | G | A | C | a | G | 75 | 3 | 14 | c | false | <90% | 1062 | ||
XR_018649 | LOC646289 | 126 | 144 | a | A | c | A | C | C | A | C | C | A | U | C | A | U | G | A | C | a | G | 75 | 3 | 14 | c | false | <90% | 1062 | ||
NM_001005289 | OR52H1 | 418 | 436 | U | A | u | A | C | C | A | C | C | A | U | C | u | U | G | A | C | U | c | 65 | 3 | 9 | false | <90% | 963 | |||
NM_012319 | SLC39A6 | 1786 | 1804 | U | u | c | A | C | C | A | C | C | A | U | C | A | U | G | A | C | U | a | 64 | 3 | 15 | bc | false | <90% | 2744 | ||
NM_022064 | RNF123 | 3962 | 3980 | a | A | A | A | C | C | A | C | C | A | U | C | g | U | G | u | C | U | G | 61 | 3 | 11 | false | <90% | 4272 | |||
XM_001133757 | LRRC48 | 1470 | 1488 | c | A | A | g | C | C | A | C | C | A | U | C | A | U | G | A | C | a | G | 58 | 3 | 13 | c | false | <90% | 2005 | ||
NM_001004727 | OR4X2 | 368 | 386 | U | A | c | A | C | C | A | C | C | A | U | C | A | U | G | A | a | c | u | 49 | 4 | 13 | c | false | <90% | 912 | ||
NM_001001955 | OR4C13 | 386 | 404 | U | A | u | A | C | C | A | C | C | A | U | C | A | U | G | A | a | g | c | 49 | 4 | 13 | c | false | <90% | 930 | ||
NM_001005490 | OR6C74 | 386 | 404 | U | A | c | A | C | C | A | C | C | A | U | C | A | U | G | A | g | c | a | 49 | 4 | 13 | c | false | <90% | 939 | ||
XM_001134223 | PKD1L3 | 3202 | 3220 | a | A | A | A | C | C | A | C | C | A | U | C | A | U | u | u | C | U | G | 47 | 3 | 13 | c | false | <90% | 5742 | ||
XM_001133467 | PKD1L3 | 3202 | 3220 | a | A | A | A | C | C | A | C | C | A | U | C | A | U | u | u | C | U | G | 47 | 3 | 13 | c | false | <90% | 5742 | ||
NM_001004451 | OR1J1 | 394 | 412 | U | A | u | g | C | C | A | C | C | A | U | C | A | U | G | A | C | U | c | 38 | 3 | 14 | bc | false | <90% | 969 | ||
NM_007249 | KLF12 | 1597 | 1615 | g | u | A | A | C | C | c | C | C | A | U | C | A | U | G | A | C | U | a | 15 | 4 | 11 | bc | false | <90% | 10923 |
3 prime UTR Seed matches
Hits to same gene : 0
Hits to other genes : 2077
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