Automatic recommendation
OK - siRNA is specific for both sense and antisense (guide) strands
5 hits were found for CCCGGGAGGUCUCGUAGAC (2 guide strand hits and 3 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_005489 | SH2D3C | 258 | 276 | C | C | C | G | a | G | A | G | G | U | C | U | C | G | g | A | G | A | C | 23 | 2 | 9 | c | false | <90% | 2164 | ||
| NM_170600 | SH2D3C | 694 | 712 | C | C | C | G | a | G | A | G | G | U | C | U | C | G | g | A | G | A | C | 23 | 2 | 9 | c | false | <90% | 3114 | ||
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_178863 | KCTD13 | 995 | 1013 | a | U | C | U | A | C | G | A | G | A | C | u | c | C | C | C | G | G | G | 53 | 3 | 10 | false | <90% | 1750 | |||
| NM_015234 | GPR116 | 4127 | 4145 | a | c | C | U | A | C | G | u | G | A | C | C | U | C | C | C | G | G | G | 24 | 3 | 11 | bc | false | <90% | 5514 | ||
| NM_015705 | RUTBC3 | 1115 | 1133 | u | U | C | U | A | C | G | A | G | g | g | C | U | C | C | C | G | G | G | -46 | 3 | 8 | c | false | <90% | 3004 | ||
3 prime UTR Seed matches
Hits to same gene : 0
Hits to other genes : 1314
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