Automatic recommendation
OK - siRNA is specific for both sense and antisense (guide) strands
35 hits were found for CCUGCACGACUCCUGCUCA (12 guide strand hits and 23 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_002457 | MUC2 | 3252 | 3270 | u | g | U | G | C | A | C | G | A | C | U | C | g | U | G | C | U | C | c | 71 | 4 | 10 | false | <90% | 15728 | |||
NM_013233 | STK39 | 2043 | 2061 | g | C | U | G | C | A | C | G | A | C | U | g | u | U | G | C | U | C | A | 53 | 3 | 10 | false | <90% | 3288 | |||
NM_009586 | SIM2 | 653 | 671 | C | C | U | G | u | A | C | G | A | C | U | C | C | U | G | C | U | a | c | 40 | 3 | 12 | c | false | <90% | 2823 | ||
NM_005069 | SIM2 | 653 | 671 | C | C | U | G | u | A | C | G | A | C | U | C | C | U | G | C | U | a | c | 40 | 3 | 12 | c | false | <90% | 3885 | ||
NM_015030 | FRYL | 7115 | 7133 | C | C | U | G | C | A | u | G | A | C | U | C | C | U | u | C | U | C | A | 9 | 2 | 7 | c | false | <90% | 11706 | ||
NM_173495 | PTCHD1 | 1995 | 2013 | C | C | U | G | C | A | C | a | A | C | U | C | C | U | G | C | a | u | c | 6 | 4 | 8 | c | false | <90% | 2682 | ||
NM_182549 | HLA-DQB2 | 684 | 702 | C | C | U | G | C | A | g | G | A | C | U | C | C | U | G | C | a | C | u | 5 | 3 | 9 | c | false | <90% | 1092 | ||
NM_130847 | AMOTL1 | 2866 | 2884 | u | g | a | G | C | A | C | G | A | C | c | C | C | U | G | C | U | C | A | 5 | 4 | 8 | c | false | <90% | 8999 | ||
XM_001127571 | PARP10 | 340 | 358 | C | C | U | G | C | A | C | G | c | C | U | g | C | U | G | C | U | C | c | 1 | 3 | 8 | false | <90% | 3360 | |||
NM_032789 | PARP10 | 330 | 348 | C | C | U | G | C | A | C | G | c | C | U | g | C | U | G | C | U | C | c | 1 | 3 | 8 | false | <90% | 3470 | |||
XM_001131379 | FCGBP | 7614 | 7632 | C | C | U | G | C | A | u | G | g | C | U | C | C | U | G | C | U | C | c | -31 | 3 | 9 | bc | false | <90% | 9378 | ||
NM_003890 | FCGBP | 14627 | 14645 | C | C | U | G | C | A | u | G | g | C | U | C | C | U | G | C | U | C | c | -31 | 3 | 9 | bc | false | <90% | 16382 |
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_014654 | SDC3 | 315 | 333 | c | G | A | G | C | A | G | G | A | G | U | C | G | g | G | C | A | u | u | 70 | 4 | 12 | c | false | <90% | 1463 | ||
XM_940667 | SDC3 | 336 | 354 | c | G | A | G | C | A | G | G | A | G | U | C | G | g | G | C | A | u | u | 70 | 4 | 12 | c | false | <90% | 5147 | ||
NM_022124 | CDH23 | 6797 | 6815 | g | G | A | G | C | A | G | G | A | G | U | C | c | U | a | C | A | G | G | 62 | 3 | 11 | false | <90% | 11073 | |||
NM_170712 | RASSF1 | 1123 | 1141 | g | c | A | G | C | A | G | G | A | G | U | g | G | U | G | C | A | G | a | 47 | 4 | 9 | false | <90% | 1674 | |||
NM_170713 | RASSF1 | 1219 | 1237 | g | c | A | G | C | A | G | G | A | G | U | g | G | U | G | C | A | G | a | 47 | 4 | 9 | false | <90% | 1770 | |||
NM_007182 | RASSF1 | 1415 | 1433 | g | c | A | G | C | A | G | G | A | G | U | g | G | U | G | C | A | G | a | 47 | 4 | 9 | false | <90% | 1968 | |||
NM_170714 | RASSF1 | 1427 | 1445 | g | c | A | G | C | A | G | G | A | G | U | g | G | U | G | C | A | G | a | 47 | 4 | 9 | false | <90% | 1979 | |||
NM_182697 | UBE2H | 16 | 34 | U | G | A | G | C | A | G | G | A | G | U | C | G | U | c | C | g | c | u | 44 | 4 | 14 | c | false | <90% | 2635 | ||
NM_003344 | UBE2H | 16 | 34 | U | G | A | G | C | A | G | G | A | G | U | C | G | U | c | C | g | c | u | 44 | 4 | 14 | c | false | <90% | 2728 | ||
NM_018186 | C1orf112 | 2386 | 2404 | U | G | A | G | C | A | G | G | A | G | U | C | G | U | a | C | u | u | u | 44 | 4 | 14 | c | false | <90% | 3363 | ||
XM_001131388 | LOC730349 | 1247 | 1265 | a | G | A | G | g | A | G | G | A | G | U | C | c | U | G | C | A | G | G | 36 | 3 | 7 | false | <90% | 1662 | |||
XM_001127633 | LOC730885 | 1247 | 1265 | a | G | A | G | g | A | G | G | A | G | U | C | c | U | G | C | A | G | G | 36 | 3 | 7 | false | <90% | 1662 | |||
XM_001128010 | LOC728646 | 1268 | 1286 | a | G | A | G | g | A | G | G | A | G | U | C | c | U | G | C | A | G | G | 36 | 3 | 7 | false | <90% | 1683 | |||
NM_198455 | SSPO | 1478 | 1496 | a | G | A | G | g | A | G | G | A | G | U | C | c | U | G | C | A | G | G | 36 | 3 | 7 | false | <90% | 15580 | |||
NM_003980 | MAP7 | 1828 | 1846 | U | G | A | G | g | A | G | G | A | G | U | C | G | c | G | C | A | G | G | 29 | 2 | 8 | c | false | <90% | 4018 | ||
XM_001128055 | BNC1 | 1725 | 1743 | U | G | A | G | C | A | G | G | A | G | g | C | c | U | G | C | A | G | u | 23 | 3 | 10 | false | <90% | 2676 | |||
NM_001717 | BNC1 | 1813 | 1831 | U | G | A | G | C | A | G | G | A | G | g | C | c | U | G | C | A | G | u | 23 | 3 | 10 | false | <90% | 4612 | |||
NM_052867 | NALCN | 4949 | 4967 | a | c | A | G | C | A | G | c | A | G | U | C | G | U | G | C | A | G | u | 19 | 4 | 10 | bc | false | <90% | 6923 | ||
NM_004758 | BZRAP1 | 4712 | 4730 | U | G | A | G | C | A | G | G | A | G | g | C | G | g | G | C | A | G | c | 14 | 3 | 10 | c | false | <90% | 7033 | ||
NM_002420 | TRPM1 | 3644 | 3662 | U | G | A | G | C | A | G | c | A | G | U | C | G | U | c | C | A | G | c | 8 | 3 | 7 | c | false | <90% | 5428 | ||
NM_016383 | LUZP4 | 370 | 388 | U | G | A | G | C | A | G | G | A | G | a | a | G | U | G | C | A | G | u | 0 | 3 | 10 | false | <90% | 1745 | |||
NM_031292 | PUS7L | 1726 | 1744 | g | G | A | G | C | A | a | G | A | G | U | a | G | U | G | C | A | G | G | -2 | 3 | 7 | false | <90% | 3959 | |||
NM_014840 | NUAK1 | 2675 | 2693 | g | G | A | G | C | A | G | G | A | c | U | u | G | U | G | C | A | G | G | -18 | 3 | 8 | false | <90% | 6821 |
3 prime UTR Seed matches
Hits to same gene : 0
Hits to other genes : 2567
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