Automatic recommendation
OK - siRNA is specific for both sense and antisense (guide) strands
14 hits were found for AUUAGAGAGCAGAUCUCUG (6 guide strand hits and 8 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_013390 | TMEM2 | 4525 | 4543 | u | U | c | A | G | A | G | A | G | C | A | G | A | U | C | U | C | U | u | 73 | 3 | 15 | bc | false | <90% | 6147 | ||
| NM_004397 | DDX6 | 2954 | 2972 | u | g | U | A | G | A | G | A | G | C | A | G | A | U | u | U | C | U | a | 56 | 4 | 12 | c | false | <90% | 4180 | ||
| NM_001963 | EGF | 987 | 1005 | u | U | U | A | u | A | G | A | G | C | A | G | A | U | C | U | C | g | a | 38 | 4 | 12 | c | false | <90% | 4877 | ||
| NM_004441 | EPHB1 | 856 | 874 | g | g | c | A | G | A | G | A | G | C | A | c | A | U | C | U | C | U | G | 33 | 4 | 8 | false | <90% | 4536 | |||
| NM_018933 | PCDHB13 | 929 | 947 | u | a | U | A | G | A | G | u | G | C | A | G | A | U | C | U | C | U | G | 24 | 3 | 11 | bc | false | <90% | 3485 | ||
| NM_019111 | HLA-DRA | 870 | 888 | c | U | U | A | G | A | G | A | G | a | A | G | A | U | C | a | C | U | G | -10 | 3 | 8 | c | false | <90% | 1267 | ||
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_145007 | NLRP11 | 1961 | 1979 | g | A | G | A | G | A | U | C | U | G | C | U | C | U | C | U | u | u | U | 71 | 3 | 15 | ac | false | <90% | 3434 | ||
| NM_002599 | PDE2A | 1439 | 1457 | C | A | G | A | G | A | U | C | U | G | C | U | C | U | g | U | g | u | U | 49 | 3 | 14 | c | false | <90% | 4240 | ||
| NM_001023562 | LOC441257 | 219 | 237 | C | u | G | A | c | A | U | C | U | G | C | U | C | U | C | U | A | A | U | 37 | 2 | 14 | bc | false | <90% | 2039 | ||
| XM_001129414 | LOC731751 | 10775 | 10793 | C | u | u | A | G | A | U | C | a | G | C | U | C | U | C | U | A | A | U | 8 | 3 | 10 | bc | false | <90% | 12650 | ||
| NM_001081640 | PRKDC | 10783 | 10801 | C | u | u | A | G | A | U | C | a | G | C | U | C | U | C | U | A | A | U | 8 | 3 | 10 | bc | false | <90% | 13416 | ||
| NM_006904 | PRKDC | 10783 | 10801 | C | u | u | A | G | A | U | C | a | G | C | U | C | U | C | U | A | A | U | 8 | 3 | 10 | bc | false | <90% | 13509 | ||
| NM_001549 | IFIT3 | 1515 | 1533 | C | A | G | A | G | A | g | C | U | c | C | U | C | U | C | U | A | A | c | -54 | 3 | 8 | bc | false | <90% | 1975 | ||
| NM_001031683 | IFIT3 | 1514 | 1532 | C | A | G | A | G | A | g | C | U | c | C | U | C | U | C | U | A | A | c | -54 | 3 | 8 | bc | false | <90% | 1999 | ||
3 prime UTR Seed matches
Hits to same gene : 0
Hits to other genes : 1535
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