Automatic recommendation
OK - siRNA is specific for both sense and antisense (guide) strands
10 hits were found for GUACAGGGAUAAACAUUAC (2 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_173674 | DCBLD1 | 1477 | 1495 | c | c | A | C | A | G | G | a | A | U | A | A | A | C | A | U | U | A | C | 24 | 3 | 11 | bc | false | <90% | 2010 | ||
| NM_019043 | APBB1IP | 2455 | 2473 | G | U | A | C | A | G | G | c | A | U | A | A | c | C | A | U | U | A | a | 22 | 3 | 7 | false | <90% | 2659 | |||
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_018101 | CDCA8 | 1656 | 1674 | u | U | u | A | U | G | U | U | U | A | U | C | C | C | U | G | U | u | u | 70 | 4 | 14 | c | false | <90% | 2319 | ||
| NM_019020 | TBC1D16 | 3071 | 3089 | G | U | A | A | U | G | U | U | U | A | U | C | C | g | U | u | U | A | a | 49 | 3 | 13 | c | false | <90% | 3303 | ||
| NM_021903 | GABBR1 | 3532 | 3550 | u | c | c | A | U | G | U | U | U | A | U | C | C | a | U | G | U | A | C | 47 | 4 | 10 | c | false | <90% | 4039 | ||
| NM_021904 | GABBR1 | 3752 | 3770 | u | c | c | A | U | G | U | U | U | A | U | C | C | a | U | G | U | A | C | 47 | 4 | 10 | c | false | <90% | 4260 | ||
| NM_021905 | GABBR1 | 3786 | 3804 | u | c | c | A | U | G | U | U | U | A | U | C | C | a | U | G | U | A | C | 47 | 4 | 10 | c | false | <90% | 4294 | ||
| NM_001470 | GABBR1 | 3938 | 3956 | u | c | c | A | U | G | U | U | U | A | U | C | C | a | U | G | U | A | C | 47 | 4 | 10 | c | false | <90% | 4445 | ||
| NM_003590 | CUL3 | 2886 | 2904 | a | c | A | A | c | G | U | U | U | A | U | C | C | C | U | G | U | A | g | 30 | 4 | 13 | bc | false | <90% | 6787 | ||
| NM_178585 | WDFY3 | 267 | 285 | a | U | A | A | U | c | U | U | U | u | U | C | C | C | U | G | U | A | C | -48 | 3 | 9 | bc | false | <90% | 4650 | ||
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