Automatic recommendation
OK - siRNA is specific for both sense and antisense (guide) strands
13 hits were found for CGUAACGGGCAACUCUGCA (5 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_002702 | POU6F1 | 2727 | 2745 | g | c | a | A | A | C | G | G | G | C | A | A | C | U | C | U | G | g | A | 64 | 4 | 14 | c | false | <90% | 2911 | ||
| NM_177404 | MAGEB1 | 790 | 808 | C | u | U | A | A | a | G | G | G | C | A | A | C | U | C | U | G | C | c | 20 | 3 | 12 | bc | false | <90% | 1722 | ||
| NM_177415 | MAGEB1 | 864 | 882 | C | u | U | A | A | a | G | G | G | C | A | A | C | U | C | U | G | C | c | 20 | 3 | 12 | bc | false | <90% | 1782 | ||
| NM_002363 | MAGEB1 | 947 | 965 | C | u | U | A | A | a | G | G | G | C | A | A | C | U | C | U | G | C | c | 20 | 3 | 12 | bc | false | <90% | 1865 | ||
| NM_016323 | HERC5 | 1739 | 1757 | a | G | U | A | u | u | G | G | G | C | A | A | C | U | C | U | G | C | A | -16 | 3 | 13 | bc | false | <90% | 3525 | ||
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_023928 | AACS | 542 | 560 | g | a | C | A | G | A | G | U | U | G | C | C | C | u | U | U | A | C | a | 62 | 4 | 11 | c | false | <90% | 3341 | ||
| NM_001033520 | WIPI2 | 3778 | 3796 | c | G | C | u | G | A | G | U | U | G | C | C | C | G | U | U | A | g | a | 53 | 4 | 13 | c | false | <90% | 4295 | ||
| NM_001033519 | WIPI2 | 3885 | 3903 | c | G | C | u | G | A | G | U | U | G | C | C | C | G | U | U | A | g | a | 53 | 4 | 13 | c | false | <90% | 4402 | ||
| NM_016003 | WIPI2 | 3918 | 3936 | c | G | C | u | G | A | G | U | U | G | C | C | C | G | U | U | A | g | a | 53 | 4 | 13 | c | false | <90% | 4435 | ||
| NM_001033518 | WIPI2 | 3939 | 3957 | c | G | C | u | G | A | G | U | U | G | C | C | C | G | U | U | A | g | a | 53 | 4 | 13 | c | false | <90% | 4456 | ||
| NM_015610 | WIPI2 | 3972 | 3990 | c | G | C | u | G | A | G | U | U | G | C | C | C | G | U | U | A | g | a | 53 | 4 | 13 | c | false | <90% | 4489 | ||
| NM_025256 | EHMT2 | 3200 | 3218 | U | G | C | A | u | A | G | a | U | G | C | C | C | G | U | U | A | C | u | -18 | 3 | 10 | bc | false | <90% | 3892 | ||
| NM_006709 | EHMT2 | 3302 | 3320 | U | G | C | A | u | A | G | a | U | G | C | C | C | G | U | U | A | C | u | -18 | 3 | 10 | bc | false | <90% | 3994 | ||
3 prime UTR Seed matches
Hits to same gene : 0
Hits to other genes : 48
View matched accessions
3 prime seed match details
| Accession | Gene name | Hits to this gene |
| NM_139072 | DNER | 2 |
| NM_198935 | SS18L1 | 1 |
| NM_014757 | MAML1 | 1 |
| XM_001126853 | MAML1 | 1 |
| NM_152311 | CLRN3 | 1 |
| NM_053041 | COMMD7 | 1 |
| NM_001099339 | 1 | |
| NM_006572 | GNA13 | 1 |
| NM_031886 | KCNA7 | 1 |
| NM_001083591 | CUGBP2 | 1 |
| NM_001025077 | CUGBP2 | 1 |
| NM_006561 | CUGBP2 | 1 |
| NM_001025076 | CUGBP2 | 1 |
| NM_001430 | EPAS1 | 1 |
| NM_145006 | SUSD3 | 1 |
| NM_032421 | CLIP2 | 1 |
| NM_003388 | CLIP2 | 1 |
| NM_001042682 | RERE | 1 |
| NM_012102 | RERE | 1 |
| NM_001042681 | RERE | 1 |
| NM_015553 | PIP3-E | 1 |
| NM_001039618 | CREBZF | 1 |
| NM_199000 | LHFPL3 | 1 |
| NM_015206 | KIAA1024 | 1 |
| NM_000842 | GRM5 | 1 |
| NM_199427 | ZFP64 | 1 |
| NM_002705 | PPL | 1 |
| NM_014643 | 1 | |
| NM_006698 | BLCAP | 1 |
| NM_030927 | TSPAN14 | 1 |
| NM_001008539 | SLC7A2 | 1 |
| NM_003046 | SLC7A2 | 1 |
| NM_005178 | BCL3 | 1 |
| NM_199454 | PRDM16 | 1 |
| NM_022114 | PRDM16 | 1 |
| NM_199054 | MKNK2 | 1 |
| NM_003262 | TLOC1 | 1 |
| NM_033647 | HELB | 1 |
| NM_022081 | HPS4 | 1 |
| NM_152841 | HPS4 | 1 |
| NM_001012241 | 1 | |
| NM_001032392 | PLGLB1 | 1 |
| NM_002665 | PLGLB2 | 1 |
| NM_006544 | EXOC5 | 1 |
| XM_378742 | FLJ45994 | 1 |
| XM_943185 | FLJ45994 | 1 |
| NM_014415 | ZBTB11 | 1 |
| NM_032440 | LCOR | 1 |
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