Automatic recommendation
OK - siRNA is specific for both sense and antisense (guide) strands
38 hits were found for GUGGCUGCGUUGGCGGCCU (17 guide strand hits and 21 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 | |||||||||||||
XM_376049 | LOC400950 | 626 | 644 | a | g | G | G | C | U | G | C | G | U | U | G | G | u | G | G | C | C | c | 62 | 4 | 11 | c | false | <90% | 3715 | ||
XM_941162 | LOC400950 | 626 | 644 | a | g | G | G | C | U | G | C | G | U | U | G | G | u | G | G | C | C | c | 62 | 4 | 11 | c | false | <90% | 3715 | ||
NM_033278 | TRIM3 | 1054 | 1072 | c | U | G | G | C | U | G | C | a | U | U | G | G | C | G | G | C | a | c | 30 | 4 | 8 | c | false | <90% | 2894 | ||
NM_006458 | TRIM3 | 1219 | 1237 | c | U | G | G | C | U | G | C | a | U | U | G | G | C | G | G | C | a | c | 30 | 4 | 8 | c | false | <90% | 3059 | ||
NM_024866 | ADM2 | 3793 | 3811 | G | a | a | G | u | U | G | C | G | U | U | G | G | C | G | G | C | C | U | 17 | 3 | 14 | bc | false | <90% | 4246 | ||
NM_001031714 | C14orf173 | 2547 | 2565 | G | U | G | G | C | U | G | a | G | U | U | G | G | g | G | G | C | C | c | 13 | 3 | 7 | c | false | <90% | 2962 | ||
NM_022489 | C14orf173 | 2604 | 2622 | G | U | G | G | C | U | G | a | G | U | U | G | G | g | G | G | C | C | c | 13 | 3 | 7 | c | false | <90% | 3019 | ||
NM_002566 | P2RY11 | 937 | 955 | G | U | G | G | C | a | G | C | G | U | U | G | G | u | G | G | C | C | a | 12 | 3 | 7 | c | false | <90% | 1977 | ||
NM_001040664 | PPAN-P2RY11 | 1996 | 2014 | G | U | G | G | C | a | G | C | G | U | U | G | G | u | G | G | C | C | a | 12 | 3 | 7 | c | false | <90% | 2385 | ||
NM_024613 | PLEKHF2 | 49 | 67 | G | c | G | G | C | U | G | C | G | c | U | G | G | C | G | G | C | C | a | 0 | 3 | 8 | bc | false | <90% | 2905 | ||
NM_019105 | TNXB | 3117 | 3135 | G | g | u | G | C | U | G | C | G | c | U | G | G | C | G | G | C | C | U | -13 | 3 | 9 | bc | false | <90% | 13268 | ||
NM_013265 | C11orf2 | 966 | 984 | G | U | G | G | C | U | u | C | G | U | g | G | G | C | G | G | C | C | U | -27 | 2 | 8 | c | false | <90% | 2546 | ||
NM_145807 | LOC126147 | 202 | 220 | c | U | G | G | C | U | G | C | c | g | U | G | G | C | G | G | C | C | U | -44 | 3 | 9 | bc | false | <90% | 1898 | ||
NM_003806 | HRK | 352 | 370 | G | U | G | G | C | g | G | C | G | c | U | G | G | C | G | G | C | C | U | -46 | 2 | 9 | bc | false | <90% | 716 | ||
XM_001128950 | LOC149478 | 571 | 589 | G | U | G | G | C | U | G | a | G | g | U | G | G | C | G | G | C | C | c | -49 | 3 | 8 | bc | false | <90% | 1308 | ||
XM_001132650 | LOC149478 | 571 | 589 | G | U | G | G | C | U | G | a | G | g | U | G | G | C | G | G | C | C | c | -49 | 3 | 8 | bc | false | <90% | 1308 | ||
NM_175885 | MGC33846 | 691 | 709 | G | U | G | G | C | U | G | C | G | c | c | G | G | C | G | G | C | C | g | -49 | 3 | 9 | c | false | <90% | 1875 |
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_016531 | KLF3 | 150 | 168 | c | G | G | C | C | G | C | C | A | A | C | G | C | c | G | C | C | c | g | 70 | 4 | 12 | c | false | <90% | 2871 | ||
NM_004977 | KCNC3 | 923 | 941 | g | c | G | C | C | G | C | C | A | A | C | G | C | c | G | C | C | A | a | 62 | 4 | 11 | c | false | <90% | 3176 | ||
NM_001013690 | LOC401720 | 124 | 142 | g | G | G | u | C | G | C | C | A | A | C | G | C | u | G | C | C | A | C | 41 | 3 | 9 | c | false | <90% | 4533 | ||
NM_021102 | SPINT2 | 733 | 751 | g | c | a | C | C | G | C | C | A | A | C | G | C | A | G | u | C | A | C | 40 | 4 | 12 | c | false | <90% | 1571 | ||
NM_002754 | MAPK13 | 50 | 68 | g | G | G | C | C | G | C | g | A | A | C | G | C | A | G | C | C | g | C | 33 | 3 | 9 | c | false | <90% | 1888 | ||
NM_016642 | SPTBN5 | 2352 | 2370 | A | G | G | C | C | c | C | C | A | A | C | G | C | A | G | C | C | g | g | 29 | 3 | 11 | c | false | <90% | 11739 | ||
NM_014299 | BRD4 | 329 | 347 | A | G | c | C | a | G | C | C | A | A | C | G | C | A | G | C | C | A | g | 23 | 3 | 13 | bc | false | <90% | 4635 | ||
NM_058243 | BRD4 | 329 | 347 | A | G | c | C | a | G | C | C | A | A | C | G | C | A | G | C | C | A | g | 23 | 3 | 13 | bc | false | <90% | 5198 | ||
NM_003614 | GALR3 | 951 | 969 | c | G | G | C | C | G | C | C | g | A | C | G | C | c | G | C | C | A | C | 18 | 3 | 7 | c | false | <90% | 1157 | ||
NM_015005 | KIAA0284 | 3752 | 3770 | A | G | G | C | u | G | C | C | A | A | C | a | C | A | G | C | C | A | C | 14 | 2 | 7 | false | <90% | 6568 | |||
XM_001133384 | LOC730263 | 1740 | 1758 | A | G | c | C | C | G | C | C | A | A | g | G | C | A | G | C | C | A | u | 14 | 3 | 7 | c | false | <90% | 2124 | ||
NM_000332 | ATXN1 | 2593 | 2611 | A | G | G | C | C | G | C | C | u | A | C | c | C | A | G | C | C | A | u | 1 | 3 | 8 | false | <90% | 10692 | |||
XM_001130543 | LOC728636 | 456 | 474 | u | G | G | C | C | c | C | C | A | A | C | c | C | A | G | C | C | A | C | 0 | 3 | 7 | false | <90% | 11548 | |||
XM_928707 | LOC642346 | 456 | 474 | u | G | G | C | C | c | C | C | A | A | C | c | C | A | G | C | C | A | C | 0 | 3 | 7 | false | <90% | 11585 | |||
NR_003246 | FLJ40113 | 167 | 185 | u | G | G | C | C | c | C | C | A | A | C | c | C | A | G | C | C | A | C | 0 | 3 | 7 | false | <90% | 13179 | |||
XM_942468 | LOC652802 | 161 | 179 | c | c | G | C | C | G | C | C | A | u | C | G | C | A | G | C | C | A | g | -1 | 4 | 8 | bc | false | <90% | 342 | ||
NM_138439 | LOC114984 | 697 | 715 | A | G | G | C | C | a | C | C | A | A | C | c | C | A | G | C | C | A | u | -2 | 3 | 6 | false | <90% | 897 | |||
NM_033502 | TRERF1 | 273 | 291 | A | G | G | C | C | c | C | C | A | A | C | u | C | A | G | C | C | A | u | -2 | 3 | 6 | false | <90% | 4395 | |||
NM_001079518 | THRAP4 | 302 | 320 | u | G | G | C | C | G | C | C | A | c | C | G | C | u | G | C | C | A | C | -4 | 3 | 8 | c | false | <90% | 3718 | ||
NM_014815 | THRAP4 | 280 | 298 | u | G | G | C | C | G | C | C | A | c | C | G | C | u | G | C | C | A | C | -4 | 3 | 8 | c | false | <90% | 3735 | ||
NM_001406 | EFNB3 | 320 | 338 | A | G | G | C | a | G | C | C | A | A | g | G | C | A | G | C | C | A | C | -12 | 2 | 8 | c | false | <90% | 3236 |
3 prime UTR Seed matches
Hits to same gene : 0
Hits to other genes : 3157
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