Automatic recommendation
OK - siRNA is specific for both sense and antisense (guide) strands
14 hits were found for GCUCUUGGACUGCAUGAAU (4 guide strand hits and 10 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_015313 | ARHGEF12 | 7481 | 7499 | u | a | a | C | U | U | G | G | A | C | U | G | C | u | U | G | A | A | U | 47 | 4 | 10 | c | false | <90% | 9501 | ||
| NM_003634 | NIPSNAP1 | 656 | 674 | c | C | U | C | a | U | G | G | A | C | U | G | C | A | U | G | A | A | c | 41 | 3 | 13 | bc | false | <90% | 2233 | ||
| NM_001870 | CPA3 | 626 | 644 | a | C | U | C | U | U | G | G | A | C | c | G | a | A | U | G | A | A | U | 26 | 3 | 9 | false | <90% | 1633 | |||
| NM_080751 | TMC2 | 2852 | 2870 | u | C | U | C | U | U | G | G | A | a | U | G | C | A | U | G | A | A | c | 10 | 3 | 8 | bc | false | <90% | 3169 | ||
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_020845 | PITPNM2 | 746 | 764 | g | g | g | C | A | U | G | C | A | G | U | C | C | A | A | G | A | u | C | 64 | 4 | 14 | c | false | <90% | 6754 | ||
| NM_004807 | HS6ST1 | 1055 | 1073 | c | U | U | C | A | U | G | C | A | G | U | a | C | A | A | u | A | G | C | 38 | 3 | 10 | false | <90% | 2051 | |||
| XM_001132928 | LOC728969 | 1062 | 1080 | c | U | U | C | A | U | G | C | A | G | U | a | C | A | A | c | A | G | C | 38 | 3 | 10 | false | <90% | 4055 | |||
| NM_053028 | MYLK | 559 | 577 | A | U | U | C | A | U | G | C | u | G | U | C | C | A | u | G | A | G | g | 10 | 3 | 8 | c | false | <90% | 7492 | ||
| NM_053026 | MYLK | 559 | 577 | A | U | U | C | A | U | G | C | u | G | U | C | C | A | u | G | A | G | g | 10 | 3 | 8 | c | false | <90% | 7645 | ||
| NM_053027 | MYLK | 559 | 577 | A | U | U | C | A | U | G | C | u | G | U | C | C | A | u | G | A | G | g | 10 | 3 | 8 | c | false | <90% | 7699 | ||
| NM_053025 | MYLK | 559 | 577 | A | U | U | C | A | U | G | C | u | G | U | C | C | A | u | G | A | G | g | 10 | 3 | 8 | c | false | <90% | 7852 | ||
| NM_173851 | SLC30A8 | 2179 | 2197 | A | U | U | C | A | U | u | C | A | G | U | C | C | A | c | G | A | G | C | 9 | 2 | 7 | c | false | <90% | 5373 | ||
| NM_023014 | PRAMEF2 | 1416 | 1434 | A | U | U | C | A | g | G | C | A | G | c | C | C | A | A | G | A | G | g | -29 | 3 | 7 | c | false | <90% | 1642 | ||
| NM_003978 | PSTPIP1 | 1164 | 1182 | u | U | U | C | A | U | c | C | A | G | g | C | C | A | A | G | A | G | C | -29 | 3 | 8 | c | false | <90% | 1781 | ||
3 prime UTR Seed matches
Hits to same gene : 0
Hits to other genes : 2172
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