Automatic recommendation
OK - siRNA is specific for both sense and antisense (guide) strands
14 hits were found for GAAUCCUCACAAUACCGCA (11 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_194298 | SLC16A9 | 3194 | 3212 | a | A | A | U | C | C | U | C | A | C | A | A | U | A | C | C | u | C | u | 69 | 3 | 15 | ac | false | <90% | 3645 | ||
| NM_152615 | PARP15 | 1244 | 1262 | G | A | A | U | C | C | U | C | A | C | A | A | U | c | C | C | a | C | A | 56 | 2 | 13 | c | false | <90% | 1956 | ||
| XM_942427 | C1orf34 | 528 | 546 | c | A | g | U | C | C | U | C | A | C | A | A | U | A | C | u | G | C | A | 52 | 3 | 12 | c | false | <90% | 2801 | ||
| XM_930328 | C1orf34 | 528 | 546 | c | A | g | U | C | C | U | C | A | C | A | A | U | A | C | u | G | C | A | 52 | 3 | 12 | c | false | <90% | 2801 | ||
| XM_945965 | C1orf34 | 595 | 613 | c | A | g | U | C | C | U | C | A | C | A | A | U | A | C | u | G | C | A | 52 | 3 | 12 | c | false | <90% | 2868 | ||
| XM_934658 | C1orf34 | 595 | 613 | c | A | g | U | C | C | U | C | A | C | A | A | U | A | C | u | G | C | A | 52 | 3 | 12 | c | false | <90% | 2868 | ||
| XM_945959 | C1orf34 | 616 | 634 | c | A | g | U | C | C | U | C | A | C | A | A | U | A | C | u | G | C | A | 52 | 3 | 12 | c | false | <90% | 2889 | ||
| NM_001080494 | C1orf34 | 616 | 634 | c | A | g | U | C | C | U | C | A | C | A | A | U | A | C | u | G | C | A | 52 | 3 | 12 | c | false | <90% | 2889 | ||
| XM_945958 | C1orf34 | 746 | 764 | c | A | g | U | C | C | U | C | A | C | A | A | U | A | C | u | G | C | A | 52 | 3 | 12 | c | false | <90% | 6268 | ||
| XM_934649 | C1orf34 | 746 | 764 | c | A | g | U | C | C | U | C | A | C | A | A | U | A | C | u | G | C | A | 52 | 3 | 12 | c | false | <90% | 6268 | ||
| NM_017831 | RNF125 | 94 | 112 | c | A | A | U | C | C | U | C | c | C | A | A | U | A | C | C | a | C | A | 14 | 3 | 7 | c | false | <90% | 5888 | ||
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_001004342 | TRIM67 | 7015 | 7033 | U | G | a | u | G | U | A | U | U | G | U | G | A | G | G | A | U | U | a | 38 | 3 | 14 | bc | false | <90% | 8522 | ||
| NM_022344 | C17orf75 | 911 | 929 | a | c | C | G | G | U | u | U | U | G | U | G | A | G | G | A | U | U | g | 15 | 4 | 11 | bc | false | <90% | 1631 | ||
| NM_014431 | KIAA1274 | 4491 | 4509 | a | G | g | G | G | U | g | U | U | G | U | G | A | G | G | A | U | U | C | 12 | 3 | 12 | bc | false | <90% | 4569 | ||
3 prime UTR Seed matches
Hits to same gene : 0
Hits to other genes : 1702
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