Automatic recommendation
Warning - siRNA is specific for only the antisense (guide) strand
33 hits were found for AUCACUCACUCUUGGCACC (17 guide strand hits and 16 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_033127 | LZTR2 | 196 | 214 | g | U | C | c | C | U | C | A | C | U | C | U | U | G | G | C | A | C | a | 56 | 3 | 14 | bc | false | <90% | 4024 | ||
NM_001001928 | PPARA | 8558 | 8576 | A | U | C | A | C | U | C | A | C | U | u | U | U | G | G | C | A | a | C | 36 | 2 | 10 | c | false | <90% | 9965 | ||
NM_005036 | PPARA | 8642 | 8660 | A | U | C | A | C | U | C | A | C | U | u | U | U | G | G | C | A | a | C | 36 | 2 | 10 | c | false | <90% | 10049 | ||
NM_014432 | IL20RA | 2671 | 2689 | A | U | C | A | C | a | C | A | C | U | C | U | U | G | G | C | u | a | C | 10 | 3 | 10 | c | false | <90% | 3682 | ||
NM_202001 | ERCC1 | 134 | 152 | c | U | C | A | C | U | C | g | C | U | C | c | U | G | G | C | A | C | C | 2 | 3 | 7 | false | <90% | 1273 | |||
NM_007298 | BRCA1 | 2039 | 2057 | A | U | C | A | u | U | C | A | C | c | C | U | U | G | G | C | A | C | a | -39 | 3 | 8 | bc | false | <90% | 3642 | ||
NM_007305 | BRCA1 | 2156 | 2174 | A | U | C | A | u | U | C | A | C | c | C | U | U | G | G | C | A | C | a | -39 | 3 | 8 | bc | false | <90% | 3759 | ||
NM_007303 | BRCA1 | 2162 | 2180 | A | U | C | A | u | U | C | A | C | c | C | U | U | G | G | C | A | C | a | -39 | 3 | 8 | bc | false | <90% | 3765 | ||
NM_007304 | BRCA1 | 2276 | 2294 | A | U | C | A | u | U | C | A | C | c | C | U | U | G | G | C | A | C | a | -39 | 3 | 8 | bc | false | <90% | 3879 | ||
NM_007300 | BRCA1 | 4793 | 4811 | A | U | C | A | u | U | C | A | C | c | C | U | U | G | G | C | A | C | a | -39 | 3 | 8 | bc | false | <90% | 6396 | ||
NM_007299 | BRCA1 | 4871 | 4889 | A | U | C | A | u | U | C | A | C | c | C | U | U | G | G | C | A | C | a | -39 | 3 | 8 | bc | false | <90% | 6474 | ||
NM_007297 | BRCA1 | 4899 | 4917 | A | U | C | A | u | U | C | A | C | c | C | U | U | G | G | C | A | C | a | -39 | 3 | 8 | bc | false | <90% | 6502 | ||
NM_007302 | BRCA1 | 5465 | 5483 | A | U | C | A | u | U | C | A | C | c | C | U | U | G | G | C | A | C | a | -39 | 3 | 8 | bc | false | <90% | 7068 | ||
NM_007296 | BRCA1 | 5582 | 5600 | A | U | C | A | u | U | C | A | C | c | C | U | U | G | G | C | A | C | a | -39 | 3 | 8 | bc | false | <90% | 7185 | ||
NM_007294 | BRCA1 | 5588 | 5606 | A | U | C | A | u | U | C | A | C | c | C | U | U | G | G | C | A | C | a | -39 | 3 | 8 | bc | false | <90% | 7191 | ||
NM_007295 | BRCA1 | 5785 | 5803 | A | U | C | A | u | U | C | A | C | c | C | U | U | G | G | C | A | C | a | -39 | 3 | 8 | bc | false | <90% | 7388 | ||
NM_080869 | WFDC12 | 380 | 398 | g | U | C | A | C | U | C | u | C | a | C | U | U | G | G | C | A | C | C | -46 | 3 | 9 | bc | false | <90% | 774 |
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 | |||||||||||||
XR_019421 | LOC126170 | 333 | 351 | a | G | U | G | C | C | A | A | G | A | G | U | G | A | G | U | G | g | U | 95 | 2 | 16 | ac | false | <90% | 480 | ||
XR_016157 | LOC126170 | 333 | 351 | a | G | U | G | C | C | A | A | G | A | G | U | G | A | G | U | G | g | U | 95 | 2 | 16 | ac | false | <90% | 480 | ||
XR_017234 | LOC402102 | 529 | 547 | a | c | U | G | C | C | A | A | G | A | G | U | G | A | G | U | G | g | U | 83 | 3 | 15 | ac | false | <90% | 675 | ||
XR_019106 | LOC651588 | 529 | 547 | a | c | U | G | C | C | A | A | G | A | G | U | G | A | G | U | G | g | U | 83 | 3 | 15 | ac | false | <90% | 675 | ||
XR_015255 | LOC730850 | 385 | 403 | a | c | U | G | C | C | A | A | G | A | G | U | G | A | G | U | G | g | U | 83 | 3 | 15 | ac | false | <90% | 793 | ||
XR_015295 | LOC728368 | 385 | 403 | a | c | U | G | C | C | A | A | G | A | G | U | G | A | G | U | G | g | U | 83 | 3 | 15 | ac | false | <90% | 793 | ||
XM_001130327 | LOC390006 | 535 | 553 | a | c | U | G | C | C | A | A | G | A | G | U | G | A | G | U | G | g | U | 83 | 3 | 15 | ac | false | <90% | 837 | ||
XM_372328 | LOC390006 | 535 | 553 | a | c | U | G | C | C | A | A | G | A | G | U | G | A | G | U | G | g | U | 83 | 3 | 15 | ac | false | <90% | 837 | ||
NM_012228 | MSRB2 | 257 | 275 | c | u | U | G | C | C | A | A | G | A | G | U | G | A | G | U | G | g | c | 78 | 4 | 15 | ac | false | <90% | 1811 | ||
NM_002044 | GALK2 | 623 | 641 | u | G | U | G | C | C | A | A | G | A | G | U | G | A | G | c | G | u | U | 69 | 3 | 14 | c | false | <90% | 3121 | ||
NM_001001556 | GALK2 | 710 | 728 | u | G | U | G | C | C | A | A | G | A | G | U | G | A | G | c | G | u | U | 69 | 3 | 14 | c | false | <90% | 3208 | ||
NM_017897 | OXSM | 374 | 392 | u | G | U | G | C | C | A | A | G | A | G | g | u | A | G | U | G | A | U | 53 | 3 | 10 | false | <90% | 1544 | |||
NM_015429 | ABI3BP | 2864 | 2882 | G | G | a | c | C | C | A | A | G | A | G | U | G | A | G | U | G | A | g | 38 | 3 | 14 | bc | false | <90% | 4533 | ||
NR_003246 | FLJ40113 | 7715 | 7733 | a | G | U | G | C | C | A | A | G | A | a | U | G | A | G | U | G | c | U | 34 | 3 | 9 | c | false | <90% | 13179 | ||
NM_025106 | SPSB1 | 2692 | 2710 | G | G | U | G | C | C | A | A | G | A | c | U | G | g | G | U | G | A | g | 14 | 3 | 10 | c | false | <90% | 3081 | ||
NM_003714 | STC2 | 2079 | 2097 | G | G | U | G | C | C | A | A | G | g | G | U | G | A | G | c | G | A | g | -13 | 3 | 9 | c | false | <90% | 5361 |
3 prime UTR Seed matches
Hits to same gene : 0
Hits to other genes : 1285
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