Automatic recommendation
OK - siRNA is specific for both sense and antisense (guide) strands
22 hits were found for GCUGAUUCUGUAUGACAAA (18 guide strand hits and 4 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_013441 | DSCR1L2 | 1355 | 1373 | c | C | U | G | A | U | U | C | U | G | U | A | U | c | A | C | A | u | g | 70 | 4 | 12 | c | false | <90% | 1700 | ||
| NM_033168 | B3GALNT1 | 2762 | 2780 | u | g | U | G | A | U | U | C | U | G | U | A | U | a | A | C | A | A | g | 62 | 4 | 11 | c | false | <90% | 3224 | ||
| NM_033169 | B3GALNT1 | 2830 | 2848 | u | g | U | G | A | U | U | C | U | G | U | A | U | a | A | C | A | A | g | 62 | 4 | 11 | c | false | <90% | 3292 | ||
| NM_003781 | B3GALNT1 | 2857 | 2875 | u | g | U | G | A | U | U | C | U | G | U | A | U | a | A | C | A | A | g | 62 | 4 | 11 | c | false | <90% | 3319 | ||
| NM_033167 | B3GALNT1 | 2976 | 2994 | u | g | U | G | A | U | U | C | U | G | U | A | U | a | A | C | A | A | g | 62 | 4 | 11 | c | false | <90% | 3438 | ||
| NM_001038628 | B3GALNT1 | 3180 | 3198 | u | g | U | G | A | U | U | C | U | G | U | A | U | a | A | C | A | A | g | 62 | 4 | 11 | c | false | <90% | 3642 | ||
| XM_939236 | LOC650155 | 1027 | 1045 | c | u | c | G | A | U | U | C | U | G | U | A | U | G | A | g | A | A | A | 40 | 4 | 12 | c | false | <90% | 2514 | ||
| XM_001132574 | LOC729092 | 1027 | 1045 | c | u | c | G | A | U | U | C | U | G | U | A | U | G | A | g | A | A | A | 40 | 4 | 12 | c | false | <90% | 4402 | ||
| XM_001132585 | LOC729092 | 1027 | 1045 | c | u | c | G | A | U | U | C | U | G | U | A | U | G | A | g | A | A | A | 40 | 4 | 12 | c | false | <90% | 4417 | ||
| XM_001132588 | LOC729092 | 1027 | 1045 | c | u | c | G | A | U | U | C | U | G | U | A | U | G | A | g | A | A | A | 40 | 4 | 12 | c | false | <90% | 4486 | ||
| NM_001083615 | MYO3B | 5155 | 5173 | c | a | U | G | A | U | U | C | a | G | U | A | U | G | A | C | A | A | A | 26 | 3 | 10 | bc | false | <90% | 5448 | ||
| NM_138995 | MYO3B | 5236 | 5254 | c | a | U | G | A | U | U | C | a | G | U | A | U | G | A | C | A | A | A | 26 | 3 | 10 | bc | false | <90% | 5529 | ||
| NM_178150 | FBXO18 | 1433 | 1451 | G | C | U | G | A | U | U | C | U | G | a | A | U | c | A | C | A | A | g | 14 | 3 | 10 | c | false | <90% | 3540 | ||
| NM_032807 | FBXO18 | 1595 | 1613 | G | C | U | G | A | U | U | C | U | G | a | A | U | c | A | C | A | A | g | 14 | 3 | 10 | c | false | <90% | 3727 | ||
| NM_001903 | CTNNA1 | 3342 | 3360 | a | C | U | G | A | U | U | C | U | c | U | A | U | G | A | C | A | u | g | 7 | 4 | 8 | c | false | <90% | 3778 | ||
| NM_005241 | EVI1 | 2766 | 2784 | u | g | c | G | A | U | U | C | U | G | g | A | U | G | A | C | A | A | A | 5 | 4 | 8 | c | false | <90% | 3570 | ||
| NM_032606 | CAPS2 | 1795 | 1813 | G | C | U | a | A | U | U | C | U | G | a | A | U | G | A | C | A | A | u | -3 | 3 | 7 | c | false | <90% | 3829 | ||
| NM_004924 | ACTN4 | 683 | 701 | G | C | U | G | A | U | U | g | a | G | U | A | U | G | A | C | A | A | g | -27 | 3 | 9 | bc | false | <90% | 3893 | ||
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_001010933 | HGF | 822 | 840 | U | g | g | a | U | C | A | U | A | C | A | G | A | A | U | C | A | G | g | 27 | 4 | 14 | bc | false | <90% | 1292 | ||
| NM_001010931 | HGF | 837 | 855 | U | g | g | a | U | C | A | U | A | C | A | G | A | A | U | C | A | G | g | 27 | 4 | 14 | bc | false | <90% | 1307 | ||
| NM_133482 | RAD50 | 5317 | 5335 | U | U | U | G | U | C | A | U | u | C | A | G | A | g | U | C | A | G | C | 20 | 2 | 8 | c | false | <90% | 5826 | ||
| NM_005732 | RAD50 | 5382 | 5400 | U | U | U | G | U | C | A | U | u | C | A | G | A | g | U | C | A | G | C | 20 | 2 | 8 | c | false | <90% | 5891 | ||
3 prime UTR Seed matches
Hits to same gene : 0
Hits to other genes : 1741
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