Automatic recommendation
OK - siRNA is specific for both sense and antisense (guide) strands
23 hits were found for CACUUCACUGCAAGACAUA (10 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_152736 | ZNF187 | 1420 | 1438 | u | u | C | U | U | C | A | C | U | G | C | A | g | G | A | C | A | U | c | 71 | 4 | 10 | false | <90% | 2328 | |||
NM_001023560 | ZNF187 | 1824 | 1842 | u | u | C | U | U | C | A | C | U | G | C | A | g | G | A | C | A | U | c | 71 | 4 | 10 | false | <90% | 2732 | |||
NM_007151 | ZNF187 | 2154 | 2172 | u | u | C | U | U | C | A | C | U | G | C | A | g | G | A | C | A | U | c | 71 | 4 | 10 | false | <90% | 3062 | |||
NM_002519 | NPAT | 3637 | 3655 | a | g | C | U | U | C | A | C | U | G | C | A | A | G | A | a | A | U | g | 55 | 4 | 13 | c | false | <90% | 5895 | ||
NM_001819 | CHGB | 2205 | 2223 | C | A | C | U | U | C | A | C | U | G | a | A | A | G | A | C | A | c | c | 31 | 3 | 10 | c | false | <90% | 2454 | ||
NM_207410 | GFRAL | 698 | 716 | C | u | C | U | U | C | A | C | a | G | C | A | A | G | A | C | A | U | g | 23 | 3 | 9 | bc | false | <90% | 1910 | ||
NM_181790 | GPR142 | 48 | 66 | C | A | C | U | U | C | c | C | U | G | C | A | g | G | A | C | A | U | c | 18 | 3 | 6 | false | <90% | 1389 | |||
NM_007054 | KIF3A | 386 | 404 | a | A | C | U | U | a | A | C | U | G | C | A | A | G | A | C | c | U | A | 11 | 3 | 10 | c | false | <90% | 6257 | ||
NM_022336 | EDAR | 2194 | 2212 | C | A | C | U | U | C | A | C | U | G | g | A | A | G | A | C | g | U | c | 10 | 3 | 10 | c | false | <90% | 4234 | ||
NM_030959 | OR12D3 | 999 | 1017 | C | A | C | U | U | C | A | C | U | G | u | A | A | G | A | a | A | U | g | 7 | 3 | 10 | c | false | <90% | 1869 |
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_017484 | ADD2 | 989 | 1007 | a | g | U | u | U | C | U | U | G | C | A | G | U | G | A | A | G | U | c | 44 | 4 | 14 | bc | false | <90% | 2877 | ||
NM_017483 | ADD2 | 989 | 1007 | a | g | U | u | U | C | U | U | G | C | A | G | U | G | A | A | G | U | c | 44 | 4 | 14 | bc | false | <90% | 3039 | ||
NM_017482 | ADD2 | 989 | 1007 | a | g | U | u | U | C | U | U | G | C | A | G | U | G | A | A | G | U | c | 44 | 4 | 14 | bc | false | <90% | 3795 | ||
NM_001617 | ADD2 | 989 | 1007 | a | g | U | u | U | C | U | U | G | C | A | G | U | G | A | A | G | U | c | 44 | 4 | 14 | bc | false | <90% | 3957 | ||
NM_017488 | ADD2 | 989 | 1007 | a | g | U | u | U | C | U | U | G | C | A | G | U | G | A | A | G | U | c | 44 | 4 | 14 | bc | false | <90% | 4043 | ||
NM_030877 | CTNNBL1 | 871 | 889 | a | c | U | G | U | a | U | U | G | C | A | G | U | G | A | A | G | U | G | 23 | 3 | 13 | bc | false | <90% | 1897 | ||
XM_001129482 | STARD9 | 10014 | 10032 | U | A | U | G | U | C | U | g | G | C | A | G | U | G | c | A | G | U | c | 8 | 3 | 7 | c | false | <90% | 15083 | ||
XM_001129290 | STARD9 | 10014 | 10032 | U | A | U | G | U | C | U | g | G | C | A | G | U | G | c | A | G | U | c | 8 | 3 | 7 | c | false | <90% | 15083 | ||
NM_207170 | SYF2 | 865 | 883 | U | A | U | u | U | C | U | U | G | u | A | G | U | G | A | A | G | U | u | -24 | 3 | 8 | bc | false | <90% | 1651 | ||
NM_015484 | SYF2 | 991 | 1009 | U | A | U | u | U | C | U | U | G | u | A | G | U | G | A | A | G | U | u | -24 | 3 | 8 | bc | false | <90% | 1777 | ||
XM_929946 | PCLO | 11315 | 11333 | c | A | U | G | U | C | U | g | a | C | A | G | U | G | A | A | G | U | G | -24 | 3 | 10 | bc | false | <90% | 15033 | ||
XM_940805 | PCLO | 11318 | 11336 | c | A | U | G | U | C | U | g | a | C | A | G | U | G | A | A | G | U | G | -24 | 3 | 10 | bc | false | <90% | 15036 | ||
XM_935710 | PCLO | 11348 | 11366 | c | A | U | G | U | C | U | g | a | C | A | G | U | G | A | A | G | U | G | -24 | 3 | 10 | bc | false | <90% | 15066 |
3 prime UTR Seed matches
Hits to same gene : 0
Hits to other genes : 2264
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