Automatic recommendation
OK - siRNA is specific for both sense and antisense (guide) strands
28 hits were found for GUUUAAAGACUGGGAGGAG (18 guide strand hits and 10 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_014991 | WDFY3 | 8718 | 8736 | G | U | a | U | A | A | A | G | A | C | U | G | G | G | A | G | G | A | u | 75 | 2 | 15 | bc | false | <90% | 14315 | ||
NM_014932 | NLGN1 | 3420 | 3438 | G | U | U | U | A | A | A | G | A | C | U | G | G | c | A | G | G | u | a | 72 | 3 | 13 | c | false | <90% | 4918 | ||
NM_152367 | C1orf161 | 1156 | 1174 | c | U | U | U | A | A | A | G | A | C | U | G | G | c | A | G | G | u | c | 70 | 4 | 12 | c | false | <90% | 3229 | ||
NM_030959 | OR12D3 | 928 | 946 | G | U | U | U | A | A | A | G | A | C | U | G | G | c | A | G | c | A | a | 51 | 3 | 13 | c | false | <90% | 1869 | ||
NR_002723 | GABPAP | 22341 | 22359 | G | g | g | U | A | A | A | G | A | C | U | G | G | a | A | G | G | A | G | 49 | 3 | 10 | c | false | <90% | 194142 | ||
NM_001024683 | ZNF688 | 373 | 391 | G | g | g | g | A | A | A | G | A | C | U | G | G | G | A | G | G | A | G | 32 | 3 | 15 | bc | false | <90% | 1151 | ||
NM_145271 | ZNF688 | 1061 | 1079 | G | g | g | g | A | A | A | G | A | C | U | G | G | G | A | G | G | A | G | 32 | 3 | 15 | bc | false | <90% | 1839 | ||
NM_001017416 | USP1 | 3304 | 3322 | u | U | U | U | A | A | A | a | A | C | U | G | G | G | A | G | G | u | c | 28 | 4 | 9 | c | false | <90% | 3424 | ||
NM_001017415 | USP1 | 3399 | 3417 | u | U | U | U | A | A | A | a | A | C | U | G | G | G | A | G | G | u | c | 28 | 4 | 9 | c | false | <90% | 3519 | ||
NM_003368 | USP1 | 3829 | 3847 | u | U | U | U | A | A | A | a | A | C | U | G | G | G | A | G | G | u | c | 28 | 4 | 9 | c | false | <90% | 3949 | ||
NM_003478 | CUL5 | 1597 | 1615 | G | U | U | g | A | A | A | G | A | C | U | u | G | G | A | G | G | A | a | 24 | 3 | 7 | false | <90% | 6408 | |||
NM_173552 | C3orf58 | 3271 | 3289 | G | U | U | U | A | A | A | a | A | C | U | G | G | a | A | G | G | A | a | 13 | 3 | 7 | c | false | <90% | 4091 | ||
NM_172219 | CSF3 | 719 | 737 | a | U | U | U | A | A | A | G | A | C | a | G | G | G | A | a | G | A | G | 10 | 3 | 9 | c | false | <90% | 1509 | ||
NM_000759 | CSF3 | 728 | 746 | a | U | U | U | A | A | A | G | A | C | a | G | G | G | A | a | G | A | G | 10 | 3 | 9 | c | false | <90% | 1518 | ||
NM_172220 | CSF3 | 895 | 913 | a | U | U | U | A | A | A | G | A | C | a | G | G | G | A | a | G | A | G | 10 | 3 | 9 | c | false | <90% | 1703 | ||
NM_000891 | KCNJ2 | 3728 | 3746 | G | U | U | U | A | A | A | G | A | g | U | u | G | G | A | G | G | A | a | -21 | 3 | 9 | false | <90% | 5397 | |||
NM_004856 | KIF23 | 1460 | 1478 | G | U | U | U | A | A | c | G | c | C | U | G | G | G | A | G | G | A | G | -26 | 2 | 10 | bc | false | <90% | 3324 | ||
NM_138555 | KIF23 | 1460 | 1478 | G | U | U | U | A | A | c | G | c | C | U | G | G | G | A | G | G | A | G | -26 | 2 | 10 | bc | false | <90% | 3636 |
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_004296 | RGS6 | 2708 | 2726 | C | U | C | C | U | C | C | C | A | G | U | C | U | U | U | A | u | c | u | 68 | 3 | 16 | ac | false | <90% | 3105 | ||
NM_021165 | FAM5B | 169 | 187 | C | U | C | C | U | C | C | C | A | G | U | C | g | U | U | g | A | A | g | 58 | 3 | 12 | false | <90% | 3617 | |||
NM_006546 | IGF2BP1 | 5728 | 5746 | C | U | C | C | U | C | C | C | A | G | U | C | c | U | U | A | u | c | a | 58 | 4 | 12 | false | <90% | 8769 | |||
NR_002776 | MCM3APAS | 2034 | 2052 | a | g | C | C | U | C | C | C | A | G | U | C | U | U | U | c | A | A | a | 55 | 4 | 13 | c | false | <90% | 2350 | ||
XM_001127102 | LOC647859 | 4884 | 4902 | C | U | u | C | U | C | C | C | A | G | U | C | U | U | U | c | A | A | g | 49 | 3 | 12 | c | false | <90% | 5226 | ||
XM_001130815 | LOC647859 | 4884 | 4902 | C | U | u | C | U | C | C | C | A | G | U | C | U | U | U | c | A | A | g | 49 | 3 | 12 | c | false | <90% | 5226 | ||
NM_015221 | DNMBP | 2272 | 2290 | C | U | C | C | U | C | C | C | A | G | U | C | U | U | c | A | u | c | a | 44 | 4 | 14 | c | false | <90% | 4734 | ||
NM_020824 | ARHGAP21 | 6297 | 6315 | u | U | C | a | U | C | C | C | u | G | U | C | U | U | U | A | A | A | C | 1 | 3 | 10 | bc | false | <90% | 7116 | ||
XR_016539 | LOC643562 | 6062 | 6080 | u | U | C | a | U | C | C | C | u | G | U | C | U | U | U | A | A | A | C | 1 | 3 | 10 | bc | false | <90% | 9549 | ||
XR_015339 | LOC730736 | 6092 | 6110 | u | U | C | a | U | C | C | C | u | G | U | C | U | U | U | A | A | A | C | 1 | 3 | 10 | bc | false | <90% | 9578 |
3 prime UTR Seed matches
Hits to same gene : 0
Hits to other genes : 4058
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