Automatic recommendation
OK - siRNA is specific for both sense and antisense (guide) strands
23 hits were found for GGAUGGAGCCUUAGAGAAA (13 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_000355 | TCN2 | 995 | 1013 | G | G | A | U | G | G | A | G | C | C | U | U | c | c | A | G | A | A | u | 65 | 3 | 12 | false | <90% | 1987 | |||
NM_058166 | TRIM6 | 656 | 674 | a | G | A | U | G | G | A | G | C | C | U | g | A | G | A | G | A | u | g | 56 | 4 | 10 | false | <90% | 3215 | |||
NM_001003818 | TRIM6 | 850 | 868 | a | G | A | U | G | G | A | G | C | C | U | g | A | G | A | G | A | u | g | 56 | 4 | 10 | false | <90% | 3409 | |||
NM_001003819 | TRIM6-TRIM34 | 850 | 868 | a | G | A | U | G | G | A | G | C | C | U | g | A | G | A | G | A | u | g | 56 | 4 | 10 | false | <90% | 3490 | |||
NM_019105 | TNXB | 5057 | 5075 | a | c | c | U | G | G | A | G | C | C | U | g | A | G | A | G | A | A | A | 33 | 4 | 8 | false | <90% | 13268 | |||
NM_031275 | TEX12 | 279 | 297 | a | G | A | U | G | a | A | G | C | C | U | U | g | G | A | G | A | A | A | 24 | 3 | 6 | false | <90% | 1144 | |||
NM_152738 | C6orf218 | 422 | 440 | a | G | A | U | G | G | A | a | C | C | U | U | A | G | u | G | A | A | A | 11 | 3 | 6 | c | false | <90% | 1147 | ||
NM_004856 | KIF23 | 1608 | 1626 | G | a | u | U | G | a | A | G | C | C | U | U | A | G | A | G | A | A | A | 5 | 3 | 13 | bc | false | <90% | 3324 | ||
NM_138555 | KIF23 | 1608 | 1626 | G | a | u | U | G | a | A | G | C | C | U | U | A | G | A | G | A | A | A | 5 | 3 | 13 | bc | false | <90% | 3636 | ||
NM_183393 | CADPS | 3059 | 3077 | G | G | A | U | G | c | A | G | C | C | U | U | A | G | A | G | g | u | g | 5 | 4 | 10 | c | false | <90% | 5248 | ||
NM_183394 | CADPS | 3179 | 3197 | G | G | A | U | G | c | A | G | C | C | U | U | A | G | A | G | g | u | g | 5 | 4 | 10 | c | false | <90% | 5372 | ||
NM_003716 | CADPS | 3149 | 3167 | G | G | A | U | G | c | A | G | C | C | U | U | A | G | A | G | g | u | g | 5 | 4 | 10 | c | false | <90% | 5489 | ||
NM_152437 | ZNF664 | 4721 | 4739 | G | c | g | U | G | G | A | G | C | a | U | U | A | G | A | G | A | A | A | -13 | 3 | 9 | bc | false | <90% | 5125 |
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_152756 | RICTOR | 5593 | 5611 | U | g | U | C | U | C | U | A | A | G | G | C | U | g | C | A | U | C | C | 69 | 2 | 11 | c | false | <90% | 9535 | ||
NM_005472 | KCNE3 | 2376 | 2394 | a | g | U | C | U | C | U | A | A | G | G | C | U | C | u | A | U | C | a | 56 | 4 | 12 | c | false | <90% | 3070 | ||
XM_932558 | LOC644982 | 1688 | 1706 | c | c | U | C | U | C | U | A | A | G | G | C | U | C | u | A | U | C | g | 56 | 4 | 12 | c | false | <90% | 3609 | ||
XM_932558 | LOC644982 | 3008 | 3026 | c | c | U | C | U | C | U | A | A | G | G | C | U | C | u | A | U | C | g | 56 | 4 | 12 | c | false | <90% | 3609 | ||
NM_005146 | SART1 | 2696 | 2714 | g | U | c | C | U | C | U | A | A | G | G | C | U | C | C | u | U | C | C | 52 | 3 | 12 | c | false | <90% | 3601 | ||
NM_183048 | ZMYND8 | 3306 | 3324 | a | U | U | C | U | C | U | u | A | G | G | C | U | C | C | A | a | C | C | 12 | 3 | 8 | c | false | <90% | 4493 | ||
NM_012408 | ZMYND8 | 3381 | 3399 | a | U | U | C | U | C | U | u | A | G | G | C | U | C | C | A | a | C | C | 12 | 3 | 8 | c | false | <90% | 4568 | ||
NM_183047 | ZMYND8 | 3381 | 3399 | a | U | U | C | U | C | U | u | A | G | G | C | U | C | C | A | a | C | C | 12 | 3 | 8 | c | false | <90% | 4652 | ||
XM_001127939 | LOC651430 | 993 | 1011 | U | U | U | C | U | C | U | A | c | G | G | C | U | C | C | A | c | u | a | 8 | 4 | 8 | c | false | <90% | 2721 | ||
XM_940582 | LOC651430 | 996 | 1014 | U | U | U | C | U | C | U | A | c | G | G | C | U | C | C | A | c | u | a | 8 | 4 | 8 | c | false | <90% | 2724 |
3 prime UTR Seed matches
Hits to same gene : 0
Hits to other genes : 2247
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