Automatic recommendation
OK - siRNA is specific for both sense and antisense (guide) strands
8 hits were found for GUACAGGUAAGAUGCUCAU (1 guide strand hits and 7 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_019072 | SGTB | 1794 | 1812 | G | U | A | a | A | G | G | U | A | g | G | A | U | G | C | U | C | A | g | -24 | 3 | 8 | bc | false | <90% | 5453 | ||
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_019555 | ARHGEF3 | 1741 | 1759 | g | c | c | u | G | C | A | U | C | U | U | A | C | C | U | G | U | A | C | 30 | 4 | 15 | bc | false | <90% | 3561 | ||
| NM_001080519 | BAHCC1 | 9000 | 9018 | g | U | G | A | G | C | A | U | C | U | c | A | C | C | U | G | U | g | u | 29 | 4 | 9 | c | false | <90% | 10708 | ||
| XM_001134463 | BAHCC1 | 9117 | 9135 | g | U | G | A | G | C | A | U | C | U | c | A | C | C | U | G | U | g | u | 29 | 4 | 9 | c | false | <90% | 10825 | ||
| NM_000603 | NOS3 | 4210 | 4228 | A | g | G | A | G | u | A | U | C | U | U | A | C | C | U | G | U | A | a | 20 | 3 | 12 | bc | false | <90% | 4341 | ||
| NM_001025109 | CD34 | 2195 | 2213 | c | U | G | A | G | C | c | U | C | U | c | A | C | C | U | G | U | A | C | -29 | 3 | 8 | c | false | <90% | 2621 | ||
| NM_001773 | CD34 | 2390 | 2408 | c | U | G | A | G | C | c | U | C | U | c | A | C | C | U | G | U | A | C | -29 | 3 | 8 | c | false | <90% | 2816 | ||
| NM_002957 | RXRA | 3389 | 3407 | u | U | G | A | G | C | c | U | C | a | U | A | C | C | U | G | U | A | C | -51 | 3 | 9 | bc | false | <90% | 5449 | ||
3 prime UTR Seed matches
Hits to same gene : 0
Hits to other genes : 1161
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