Automatic recommendation
OK - siRNA is specific for both sense and antisense (guide) strands
12 hits were found for CGGCCUAUGAAAAGAUUCU (7 guide strand hits and 5 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 | |||||||||||||
| XM_943317 | LOC150577 | 2816 | 2834 | u | G | G | C | C | U | A | U | G | A | A | A | g | G | A | U | c | C | U | 64 | 3 | 11 | false | <90% | 3113 | |||
| XM_379114 | LOC150577 | 2818 | 2836 | u | G | G | C | C | U | A | U | G | A | A | A | g | G | A | U | c | C | U | 64 | 3 | 11 | false | <90% | 3115 | |||
| NM_002349 | LY75 | 3119 | 3137 | C | u | G | C | C | U | A | U | G | A | A | A | A | G | A | U | a | a | a | 57 | 4 | 14 | ac | false | <90% | 6927 | ||
| NM_173822 | FAM126B | 2134 | 2152 | a | u | c | C | C | U | A | U | G | A | A | A | c | G | A | U | U | C | U | 56 | 4 | 9 | false | <90% | 4001 | |||
| NM_001008657 | TCOF1 | 950 | 968 | a | G | G | C | C | U | c | U | G | A | A | A | A | a | A | U | U | C | U | 12 | 3 | 6 | c | false | <90% | 3827 | ||
| NM_000356 | TCOF1 | 719 | 737 | a | G | G | C | C | U | c | U | G | A | A | A | A | a | A | U | U | C | U | 12 | 3 | 6 | c | false | <90% | 4849 | ||
| NM_001008656 | TCOF1 | 950 | 968 | a | G | G | C | C | U | c | U | G | A | A | A | A | a | A | U | U | C | U | 12 | 3 | 6 | c | false | <90% | 4966 | ||
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_001040192 | C21orf55 | 350 | 368 | g | G | A | A | U | C | U | U | U | U | C | A | U | A | a | G | C | u | u | 65 | 4 | 13 | c | false | <90% | 1609 | ||
| NM_017833 | C21orf55 | 653 | 671 | g | G | A | A | U | C | U | U | U | U | C | A | U | A | a | G | C | u | u | 65 | 4 | 13 | c | false | <90% | 1912 | ||
| NM_178834 | LAYN | 1857 | 1875 | A | G | A | A | U | C | U | U | U | U | C | A | a | A | G | c | C | C | a | 58 | 3 | 12 | false | <90% | 2066 | |||
| XM_938194 | LOC127602 | 9946 | 9964 | A | G | A | A | U | C | U | U | U | U | a | A | U | A | G | u | C | C | a | 7 | 3 | 10 | c | false | <90% | 13621 | ||
| XM_059166 | LOC127602 | 9946 | 9964 | A | G | A | A | U | C | U | U | U | U | a | A | U | A | G | u | C | C | a | 7 | 3 | 10 | c | false | <90% | 13622 | ||
3 prime UTR Seed matches
Hits to same gene : 0
Hits to other genes : 248
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