Automatic recommendation
OK - siRNA is specific for both sense and antisense (guide) strands
19 hits were found for GCAGCAAGAGGUUACAUUU (6 guide strand hits and 13 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_001522 | GUCY2F | 1267 | 1285 | G | C | A | G | C | A | A | G | A | G | G | U | g | A | a | A | U | U | c | 59 | 3 | 12 | false | <90% | 3698 | |||
| NM_016620 | ZNF644 | 192 | 210 | a | C | A | G | C | A | A | G | A | G | G | U | U | u | g | A | U | U | U | 53 | 3 | 12 | c | false | <90% | 2085 | ||
| XM_001129158 | LIMS1 | 2797 | 2815 | G | C | A | G | C | c | A | G | A | G | G | U | U | c | C | A | U | U | g | 12 | 3 | 7 | c | false | <90% | 4056 | ||
| XR_016628 | LOC196469 | 858 | 876 | c | C | A | G | C | A | A | G | u | G | G | c | U | A | C | A | U | U | U | 4 | 3 | 7 | false | <90% | 1154 | |||
| NM_014784 | ARHGEF11 | 4986 | 5004 | G | C | A | G | C | A | g | G | A | G | G | U | U | A | C | A | a | a | g | 2 | 4 | 9 | c | false | <90% | 6784 | ||
| NM_198236 | ARHGEF11 | 5106 | 5124 | G | C | A | G | C | A | g | G | A | G | G | U | U | A | C | A | a | a | g | 2 | 4 | 9 | c | false | <90% | 6904 | ||
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_001344 | DAD1 | 637 | 655 | A | A | A | U | G | U | A | A | C | C | U | u | U | U | G | C | U | u | u | 58 | 3 | 11 | false | <90% | 699 | |||
| NM_024749 | VASH2 | 2495 | 2513 | c | A | g | U | G | U | A | A | C | C | U | C | U | g | G | C | U | G | C | 58 | 3 | 10 | c | false | <90% | 3580 | ||
| XM_371891 | DPY19L1 | 2083 | 2101 | u | u | A | U | G | U | A | A | C | C | U | C | U | U | G | g | U | G | a | 55 | 4 | 13 | c | false | <90% | 4865 | ||
| XM_938743 | DPY19L1 | 2083 | 2101 | u | u | A | U | G | U | A | A | C | C | U | C | U | U | G | g | U | G | a | 55 | 4 | 13 | c | false | <90% | 4865 | ||
| XM_935726 | DPY19L1 | 2083 | 2101 | u | u | A | U | G | U | A | A | C | C | U | C | U | U | G | g | U | G | a | 55 | 4 | 13 | c | false | <90% | 4865 | ||
| NM_153487 | MDGA1 | 8841 | 8859 | A | A | A | U | G | U | A | A | C | C | U | C | U | a | G | u | U | G | C | 54 | 2 | 13 | c | false | <90% | 8907 | ||
| NM_012245 | SNW1 | 2070 | 2088 | c | A | A | a | G | U | A | A | C | C | U | C | U | U | G | C | U | u | g | 53 | 4 | 13 | c | false | <90% | 2146 | ||
| NM_024808 | C13orf34 | 1548 | 1566 | g | c | A | U | G | U | c | A | C | C | U | C | U | U | G | C | U | G | a | 15 | 4 | 11 | bc | false | <90% | 2803 | ||
| NM_152924 | ABHD2 | 33 | 51 | A | A | A | U | G | U | A | A | C | C | a | a | U | U | G | C | U | G | a | 0 | 3 | 10 | false | <90% | 8687 | |||
| NM_007011 | ABHD2 | 33 | 51 | A | A | A | U | G | U | A | A | C | C | a | a | U | U | G | C | U | G | a | 0 | 3 | 10 | false | <90% | 9085 | |||
| NM_138782 | FCHO2 | 4119 | 4137 | u | u | A | U | G | U | A | A | C | a | U | C | U | U | G | C | U | G | u | -1 | 4 | 8 | bc | false | <90% | 4909 | ||
| NM_207366 | FLJ44060 | 2243 | 2261 | u | A | A | U | G | U | A | A | C | u | U | C | U | U | a | C | U | G | C | -9 | 3 | 8 | c | false | <90% | 3073 | ||
| NM_002844 | PTPRK | 3267 | 3285 | A | A | A | U | G | g | A | A | C | C | a | C | U | U | G | C | U | G | a | -29 | 3 | 7 | c | false | <90% | 5982 | ||
3 prime UTR Seed matches
Hits to same gene : 0
Hits to other genes : 1897
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