Automatic recommendation
OK - siRNA is specific for both sense and antisense (guide) strands
9 hits were found for UUGCUUUUCGGGAUUUAUG (5 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_006071 | PKDREJ | 1574 | 1592 | U | U | G | C | U | U | U | U | C | G | G | c | A | U | U | U | u | U | u | 37 | 3 | 11 | false | <90% | 7660 | |||
| NM_139313 | YME1L1 | 1083 | 1101 | c | U | G | C | U | a | U | U | C | G | G | c | A | U | U | U | A | U | G | 0 | 3 | 7 | false | <90% | 2584 | |||
| NM_014263 | YME1L1 | 912 | 930 | c | U | G | C | U | a | U | U | C | G | G | c | A | U | U | U | A | U | G | 0 | 3 | 7 | false | <90% | 3865 | |||
| NM_139312 | YME1L1 | 1083 | 1101 | c | U | G | C | U | a | U | U | C | G | G | c | A | U | U | U | A | U | G | 0 | 3 | 7 | false | <90% | 4036 | |||
| NM_012249 | RHOQ | 2972 | 2990 | U | U | G | C | c | U | U | U | g | G | G | G | A | U | U | U | A | U | G | -11 | 2 | 10 | bc | false | <90% | 4542 | ||
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_000946 | PRIM1 | 1272 | 1290 | g | A | U | A | A | A | U | C | C | C | G | A | A | A | A | G | g | A | g | 69 | 3 | 15 | ac | false | <90% | 1471 | ||
| NM_005509 | DMXL1 | 1425 | 1443 | a | A | U | A | A | A | U | C | C | C | G | A | A | A | A | G | a | A | g | 69 | 3 | 15 | ac | false | <90% | 11072 | ||
| NM_001013687 | LOC401589 | 1576 | 1594 | C | u | U | A | A | A | U | C | C | C | c | A | A | A | A | G | C | A | c | 22 | 3 | 8 | c | false | <90% | 2369 | ||
| NM_024336 | IRX3 | 2029 | 2047 | u | A | U | A | A | A | U | a | C | C | u | A | A | A | A | G | C | A | A | -25 | 3 | 8 | c | false | <90% | 2308 | ||
3 prime UTR Seed matches
Hits to same gene : 0
Hits to other genes : 5204
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