Automatic recommendation
OK - siRNA is specific for both sense and antisense (guide) strands
14 hits were found for CUGCUGUCUACAGAAUUAA (5 guide strand hits and 9 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_000149 | FUT3 | 2415 | 2433 | C | U | G | C | U | G | U | C | U | A | C | A | a | A | A | U | g | c | c | 58 | 4 | 12 | false | <90% | 2581 | |||
| NM_024746 | KIAA1822L | 2378 | 2396 | u | U | G | C | U | G | U | C | U | A | C | u | G | A | A | U | a | A | A | 40 | 3 | 10 | false | <90% | 2582 | |||
| NM_004333 | BRAF | 645 | 663 | g | U | G | C | U | G | U | u | U | A | C | A | G | A | A | U | U | c | A | 33 | 3 | 9 | c | false | <90% | 2477 | ||
| NM_020903 | USP29 | 2661 | 2679 | a | a | u | C | a | G | U | C | U | A | C | A | G | A | A | U | U | A | A | 15 | 4 | 14 | bc | false | <90% | 3607 | ||
| NM_024698 | SLC25A22 | 2653 | 2671 | C | U | G | C | U | G | c | u | U | A | C | A | G | A | A | U | U | A | u | -33 | 3 | 10 | bc | false | <90% | 2780 | ||
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_014840 | NUAK1 | 5338 | 5356 | a | a | A | A | U | U | C | U | G | U | A | G | A | u | A | G | C | A | a | 62 | 4 | 11 | c | false | <90% | 6821 | ||
| NM_001173 | ARHGAP5 | 5564 | 5582 | U | U | A | A | U | U | C | U | G | U | A | a | A | C | A | G | a | u | G | 40 | 3 | 11 | false | <90% | 9601 | |||
| NM_001030055 | ARHGAP5 | 5567 | 5585 | U | U | A | A | U | U | C | U | G | U | A | a | A | C | A | G | a | u | G | 40 | 3 | 11 | false | <90% | 9604 | |||
| NM_012287 | CENTB2 | 2741 | 2759 | c | U | A | u | U | U | C | U | G | U | A | G | A | C | A | G | a | A | G | 37 | 3 | 12 | c | false | <90% | 7102 | ||
| NM_052817 | MID2 | 1551 | 1569 | a | U | A | A | U | U | C | a | G | U | A | G | A | C | A | G | C | u | G | 33 | 3 | 9 | c | false | <90% | 2433 | ||
| NM_012216 | MID2 | 1641 | 1659 | a | U | A | A | U | U | C | a | G | U | A | G | A | C | A | G | C | u | G | 33 | 3 | 9 | c | false | <90% | 2523 | ||
| NM_199413 | PRC1 | 1872 | 1890 | U | U | A | A | U | U | C | U | G | U | u | G | c | C | A | G | C | A | c | 23 | 3 | 10 | false | <90% | 3091 | |||
| NM_003981 | PRC1 | 1872 | 1890 | U | U | A | A | U | U | C | U | G | U | u | G | c | C | A | G | C | A | c | 23 | 3 | 10 | false | <90% | 3128 | |||
| NM_015652 | C10orf12 | 3017 | 3035 | c | U | A | A | U | U | C | U | G | a | A | G | A | C | A | G | C | A | u | 10 | 3 | 8 | bc | false | <90% | 4565 | ||
3 prime UTR Seed matches
Hits to same gene : 0
Hits to other genes : 4391
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