Automatic recommendation
OK - siRNA is specific for both sense and antisense (guide) strands
26 hits were found for AGGAGACACACACCUGUAU (13 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_001012993 | C9orf152 | 517 | 535 | A | G | G | A | G | A | C | A | C | A | C | A | C | u | U | G | U | u | U | 77 | 2 | 13 | c | false | <90% | 2162 | ||
NM_153220 | MGC35440 | 1815 | 1833 | u | G | G | u | G | A | C | A | C | A | C | A | C | C | U | G | U | A | a | 56 | 3 | 14 | bc | false | <90% | 2298 | ||
NM_177538 | CYP20A1 | 3353 | 3371 | u | G | G | u | G | A | C | A | C | A | C | A | C | C | U | G | U | A | g | 56 | 3 | 14 | bc | false | <90% | 10943 | ||
NM_001128 | AP1G1 | 3387 | 3405 | c | a | c | A | G | A | C | A | C | A | C | A | C | a | U | G | U | A | U | 47 | 4 | 10 | c | false | <90% | 6841 | ||
NM_001030007 | AP1G1 | 3396 | 3414 | c | a | c | A | G | A | C | A | C | A | C | A | C | a | U | G | U | A | U | 47 | 4 | 10 | c | false | <90% | 6850 | ||
NM_005245 | FAT | 11620 | 11638 | A | G | G | A | G | A | a | A | C | A | C | A | C | C | U | G | U | g | U | 31 | 2 | 10 | c | false | <90% | 14773 | ||
NM_003324 | TULP3 | 2036 | 2054 | g | c | G | A | c | A | C | A | C | A | C | A | C | C | U | G | U | A | g | 30 | 4 | 13 | bc | false | <90% | 2945 | ||
NM_017644 | KLHL24 | 2967 | 2985 | c | a | G | A | G | A | C | u | C | A | C | A | C | C | U | G | U | A | c | 19 | 4 | 10 | bc | false | <90% | 7331 | ||
NM_024915 | GRHL2 | 2601 | 2619 | A | G | G | A | G | A | C | A | C | A | g | A | C | C | U | G | g | A | g | 10 | 3 | 10 | c | false | <90% | 4792 | ||
NM_017893 | SEMA4G | 3718 | 3736 | u | G | G | u | a | A | C | A | C | A | C | A | C | C | U | G | U | A | U | 9 | 3 | 14 | bc | false | <90% | 4400 | ||
NM_005216 | DDOST | 1334 | 1352 | A | G | G | c | u | A | C | A | C | A | C | A | C | C | U | G | U | A | c | 6 | 3 | 13 | bc | false | <90% | 2144 | ||
NM_032932 | RAB11FIP4 | 3194 | 3212 | u | u | u | A | G | A | a | A | C | A | C | A | C | C | U | G | U | A | U | 0 | 4 | 12 | bc | false | <90% | 8665 | ||
NR_002723 | GABPAP | 93012 | 93030 | A | G | G | A | G | A | u | A | C | A | u | A | C | C | U | G | U | A | c | -32 | 3 | 7 | c | false | <90% | 194142 |
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_138287 | DTX3L | 3200 | 3218 | u | U | A | C | A | G | G | U | G | U | G | U | G | c | C | U | C | C | a | 73 | 3 | 12 | c | false | <90% | 4926 | ||
NM_024582 | FAT4 | 13094 | 13112 | c | U | A | C | A | G | G | U | G | U | G | U | c | c | C | U | C | C | U | 68 | 3 | 11 | false | <90% | 14775 | |||
NM_174900 | ZFP42 | 2059 | 2077 | c | U | A | C | A | G | G | U | G | U | G | U | G | U | C | a | C | C | a | 66 | 3 | 14 | c | false | <90% | 2646 | ||
NM_182757 | IBRDC2 | 4062 | 4080 | u | U | A | C | A | G | G | U | G | U | G | U | G | U | C | a | C | u | g | 64 | 4 | 14 | c | false | <90% | 4782 | ||
NR_003127 | ZNF542 | 5701 | 5719 | u | U | A | C | A | G | G | U | G | U | G | U | c | U | u | U | C | C | U | 62 | 3 | 11 | false | <90% | 11390 | |||
NM_145306 | C10orf35 | 644 | 662 | c | c | A | C | A | G | G | U | G | U | G | U | G | U | u | U | C | C | c | 56 | 4 | 12 | c | false | <90% | 1129 | ||
XM_937729 | TBC1D12 | 4287 | 4305 | A | a | u | C | A | G | G | U | G | U | G | U | G | U | u | U | C | C | U | 44 | 3 | 11 | c | false | <90% | 5843 | ||
XM_051081 | TBC1D12 | 4287 | 4305 | A | a | u | C | A | G | G | U | G | U | G | U | G | U | u | U | C | C | U | 44 | 3 | 11 | c | false | <90% | 5843 | ||
NM_025257 | SLC44A4 | 341 | 359 | c | c | c | C | A | G | G | U | G | U | G | U | G | U | g | U | C | C | U | 42 | 4 | 11 | c | false | <90% | 2347 | ||
NM_032794 | SLC44A4 | 358 | 376 | c | c | c | C | A | G | G | U | G | U | G | U | G | U | g | U | C | C | U | 42 | 4 | 11 | c | false | <90% | 2579 | ||
NM_002595 | PCTK2 | 857 | 875 | c | U | A | C | A | G | G | U | G | U | u | U | G | U | C | U | C | a | g | 29 | 4 | 9 | c | false | <90% | 4041 | ||
NM_001010980 | C1orf130 | 1762 | 1780 | c | U | A | C | A | G | G | U | a | U | G | U | G | U | C | a | C | C | U | 11 | 3 | 7 | c | false | <90% | 3953 | ||
NM_144966 | FREM1 | 1847 | 1865 | A | U | A | C | A | G | G | U | c | U | G | a | G | U | C | U | C | C | U | 6 | 2 | 8 | false | <90% | 7387 |
3 prime UTR Seed matches
Hits to same gene : 0
Hits to other genes : 2297
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)
Motif found in sense strand
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