Automatic recommendation
Warning - siRNA is specific for only the antisense (guide) strand
8 hits were found for GGACCAAACUUAUACAAUA (2 guide strand hits and 6 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_003794 | SNX4 | 2484 | 2502 | u | u | g | C | C | A | A | A | C | U | U | A | U | A | C | A | A | U | A | 67 | 3 | 16 | bc | false | <90% | 2567 | ||
| NM_004744 | LRAT | 3940 | 3958 | u | G | A | C | C | A | A | A | u | U | U | A | U | A | C | A | A | a | c | 30 | 4 | 8 | c | false | <90% | 4909 | ||
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_022483 | C5orf28 | 2388 | 2406 | U | A | U | U | G | U | A | U | A | A | G | U | U | U | G | G | U | u | g | 92 | 2 | 17 | ac | false | <90% | 2972 | ||
| NM_004376 | COX15 | 1394 | 1412 | a | g | U | U | G | U | A | U | A | A | G | U | U | U | G | G | g | C | u | 58 | 4 | 14 | ac | false | <90% | 2884 | ||
| NM_078470 | COX15 | 2633 | 2651 | a | g | U | U | G | U | A | U | A | A | G | U | U | U | G | G | g | C | u | 58 | 4 | 14 | ac | false | <90% | 4081 | ||
| XM_001128623 | LOC728849 | 9796 | 9814 | U | A | U | U | G | U | A | U | A | u | G | U | U | U | u | G | U | C | C | -7 | 2 | 9 | c | false | <90% | 10120 | ||
| NM_138270 | ATRX | 9911 | 9929 | U | A | U | U | G | U | A | U | A | u | G | U | U | U | u | G | U | C | C | -7 | 2 | 9 | c | false | <90% | 11088 | ||
| NM_000489 | ATRX | 10025 | 10043 | U | A | U | U | G | U | A | U | A | u | G | U | U | U | u | G | U | C | C | -7 | 2 | 9 | c | false | <90% | 11202 | ||
3 prime UTR Seed matches
Hits to same gene : 0
Hits to other genes : 1544
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