Automatic recommendation
OK - siRNA is specific for both sense and antisense (guide) strands
13 hits were found for UGUCUGAUAGAGAUCUUUA (10 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_145809 | LOC220594 | 2493 | 2511 | U | G | U | C | U | G | A | U | A | G | A | G | A | a | C | U | U | U | c | 75 | 2 | 13 | c | false | <90% | 4413 | ||
| NM_004505 | USP6 | 6107 | 6125 | U | G | U | C | U | G | A | U | A | G | A | G | A | a | C | U | U | U | c | 75 | 2 | 13 | c | false | <90% | 7971 | ||
| NR_003190 | LOC162632 | 7714 | 7732 | U | G | U | C | U | G | A | U | A | G | A | G | A | a | C | U | U | U | c | 75 | 2 | 13 | c | false | <90% | 9547 | ||
| NM_024924 | ZNF702 | 2588 | 2606 | a | a | a | C | U | G | A | U | A | G | A | G | A | U | u | U | U | U | A | 42 | 4 | 11 | c | false | <90% | 2996 | ||
| NM_005369 | MCF2 | 61 | 79 | U | G | U | u | U | G | A | U | A | G | A | G | A | U | u | U | U | U | g | 33 | 3 | 10 | c | false | <90% | 3652 | ||
| NM_139135 | ARID1A | 4889 | 4907 | U | G | c | C | U | G | A | U | u | G | A | G | A | U | C | U | U | U | g | 15 | 3 | 9 | bc | false | <90% | 7934 | ||
| NM_006015 | ARID1A | 5540 | 5558 | U | G | c | C | U | G | A | U | u | G | A | G | A | U | C | U | U | U | g | 15 | 3 | 9 | bc | false | <90% | 8585 | ||
| XM_001132824 | LOC731454 | 466 | 484 | U | G | U | C | U | G | A | c | A | G | A | G | A | c | C | U | U | U | c | 13 | 3 | 7 | c | false | <90% | 826 | ||
| XM_001130998 | LOC728626 | 466 | 484 | U | G | U | C | U | G | A | c | A | G | A | G | A | c | C | U | U | U | c | 13 | 3 | 7 | c | false | <90% | 826 | ||
| NM_003480 | MFAP5 | 1078 | 1096 | U | G | U | C | U | G | A | U | A | u | A | G | A | U | C | U | U | a | g | 9 | 3 | 9 | c | false | <90% | 2900 | ||
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_014677 | RIMS2 | 840 | 858 | c | A | A | A | G | A | U | C | U | a | U | A | U | C | A | G | A | a | c | 7 | 4 | 8 | c | false | <90% | 4451 | ||
| NR_003377 | LOC728939 | 9661 | 9679 | g | g | c | A | G | A | U | C | U | g | U | A | U | C | A | G | A | C | A | -15 | 4 | 9 | bc | false | <90% | 18232 | ||
| NM_005392 | PHF2 | 4735 | 4753 | a | A | A | A | G | A | U | C | U | a | U | u | U | C | A | G | A | C | A | -18 | 3 | 8 | false | <90% | 5349 | |||
3 prime UTR Seed matches
Hits to same gene : 0
Hits to other genes : 2425
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