Automatic recommendation
OK - siRNA is specific for both sense and antisense (guide) strands
25 hits were found for GUGGCUCCAUCUUAGCCCU (17 guide strand hits and 8 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_015879 | ST8SIA3 | 3805 | 3823 | u | U | G | G | C | U | C | C | A | U | C | U | U | A | a | C | C | u | U | 70 | 3 | 13 | c | false | <90% | 10154 | ||
NM_006766 | MYST3 | 5765 | 5783 | c | U | G | G | C | U | C | C | A | U | C | U | c | A | u | C | C | C | U | 62 | 3 | 11 | false | <90% | 7861 | |||
NM_014909 | VASH1 | 5440 | 5458 | c | U | c | G | C | U | C | C | A | U | C | U | U | g | G | C | C | C | U | 58 | 3 | 10 | c | false | <90% | 5746 | ||
NM_006393 | NEBL | 2940 | 2958 | c | U | G | G | C | U | C | C | A | U | C | U | U | c | G | a | C | C | U | 52 | 3 | 12 | c | false | <90% | 8034 | ||
NM_002733 | PRKAG1 | 1401 | 1419 | c | U | G | c | C | U | C | C | A | U | C | U | U | g | G | C | C | C | U | 41 | 3 | 9 | c | false | <90% | 1707 | ||
NM_212461 | PRKAG1 | 1450 | 1468 | c | U | G | c | C | U | C | C | A | U | C | U | U | g | G | C | C | C | U | 41 | 3 | 9 | c | false | <90% | 1756 | ||
NM_198973 | MKNK1 | 386 | 404 | G | a | G | G | u | U | C | C | A | U | C | U | U | A | G | C | C | C | a | 32 | 3 | 13 | bc | false | <90% | 1238 | ||
NM_003684 | MKNK1 | 550 | 568 | G | a | G | G | u | U | C | C | A | U | C | U | U | A | G | C | C | C | a | 32 | 3 | 13 | bc | false | <90% | 2736 | ||
NM_152918 | EMR2 | 172 | 190 | G | U | G | G | C | a | C | C | A | U | C | U | U | A | G | C | u | C | a | 8 | 3 | 10 | c | false | <90% | 6345 | ||
NM_152921 | EMR2 | 172 | 190 | G | U | G | G | C | a | C | C | A | U | C | U | U | A | G | C | u | C | a | 8 | 3 | 10 | c | false | <90% | 6459 | ||
NM_152917 | EMR2 | 172 | 190 | G | U | G | G | C | a | C | C | A | U | C | U | U | A | G | C | u | C | a | 8 | 3 | 10 | c | false | <90% | 6492 | ||
NM_152920 | EMR2 | 172 | 190 | G | U | G | G | C | a | C | C | A | U | C | U | U | A | G | C | u | C | a | 8 | 3 | 10 | c | false | <90% | 6591 | ||
NM_152916 | EMR2 | 172 | 190 | G | U | G | G | C | a | C | C | A | U | C | U | U | A | G | C | u | C | a | 8 | 3 | 10 | c | false | <90% | 6624 | ||
NM_152919 | EMR2 | 172 | 190 | G | U | G | G | C | a | C | C | A | U | C | U | U | A | G | C | u | C | a | 8 | 3 | 10 | c | false | <90% | 6738 | ||
NM_013447 | EMR2 | 172 | 190 | G | U | G | G | C | a | C | C | A | U | C | U | U | A | G | C | u | C | a | 8 | 3 | 10 | c | false | <90% | 6771 | ||
NM_032138 | KBTBD7 | 788 | 806 | G | U | G | c | C | U | C | C | u | U | C | U | U | A | G | C | C | C | g | -1 | 3 | 9 | bc | false | <90% | 3008 | ||
NM_152903 | KBTBD6 | 768 | 786 | G | U | G | c | C | U | C | C | u | U | C | U | U | A | G | C | C | C | g | -1 | 3 | 9 | bc | false | <90% | 5228 |
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_138730 | HMGN3 | 210 | 228 | A | G | G | G | C | a | A | A | G | A | U | G | G | A | u | C | C | A | a | 7 | 3 | 8 | c | false | <90% | 899 | ||
NM_004242 | HMGN3 | 210 | 228 | A | G | G | G | C | a | A | A | G | A | U | G | G | A | u | C | C | A | a | 7 | 3 | 8 | c | false | <90% | 935 | ||
NM_175634 | RUNX1T1 | 1529 | 1547 | A | G | G | G | C | c | A | A | G | A | U | G | G | A | G | C | g | c | a | 5 | 4 | 10 | c | false | <90% | 3217 | ||
NM_175635 | RUNX1T1 | 1545 | 1563 | A | G | G | G | C | c | A | A | G | A | U | G | G | A | G | C | g | c | a | 5 | 4 | 10 | c | false | <90% | 3233 | ||
NM_175636 | RUNX1T1 | 1674 | 1692 | A | G | G | G | C | c | A | A | G | A | U | G | G | A | G | C | g | c | a | 5 | 4 | 10 | c | false | <90% | 3362 | ||
NM_004349 | RUNX1T1 | 1775 | 1793 | A | G | G | G | C | c | A | A | G | A | U | G | G | A | G | C | g | c | a | 5 | 4 | 10 | c | false | <90% | 3463 | ||
NR_003266 | LOC220729 | 3285 | 3303 | A | G | G | G | C | U | c | u | G | A | U | G | G | A | G | C | C | A | g | -33 | 3 | 10 | bc | false | <90% | 15309 | ||
NM_007055 | POLR3A | 3164 | 3182 | A | G | G | G | C | a | c | A | G | A | U | G | G | A | G | C | C | A | g | -34 | 3 | 11 | bc | false | <90% | 5618 |
3 prime UTR Seed matches
Hits to same gene : 0
Hits to other genes : 3327
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