Automatic recommendation
OK - siRNA is specific for both sense and antisense (guide) strands
12 hits were found for UUGGAAUUGAUUGCGAAAG (5 guide strand hits and 7 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_153353 | LRRC34 | 478 | 496 | g | g | a | G | A | A | U | U | G | A | U | U | G | C | u | A | A | A | G | 42 | 4 | 11 | c | false | <90% | 1448 | ||
| NM_001017397 | TRIM36 | 549 | 567 | a | U | G | G | A | A | U | U | G | A | U | a | G | C | u | A | A | A | G | 39 | 3 | 10 | false | <90% | 760 | |||
| NM_001017398 | TRIM36 | 549 | 567 | a | U | G | G | A | A | U | U | G | A | U | a | G | C | u | A | A | A | G | 39 | 3 | 10 | false | <90% | 906 | |||
| NM_018700 | TRIM36 | 549 | 567 | a | U | G | G | A | A | U | U | G | A | U | a | G | C | u | A | A | A | G | 39 | 3 | 10 | false | <90% | 4456 | |||
| NM_001655 | ARCN1 | 3531 | 3549 | g | U | G | G | A | A | U | U | G | c | U | U | G | C | c | A | A | A | G | -9 | 3 | 8 | c | false | <90% | 3916 | ||
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_003845 | DYRK4 | 680 | 698 | C | U | U | U | C | G | C | A | A | U | C | A | c | U | U | C | u | g | c | 58 | 4 | 12 | false | <90% | 1860 | |||
| NM_030641 | APOL6 | 71 | 89 | g | U | U | U | u | G | C | A | A | U | C | A | A | U | U | C | C | u | g | 38 | 4 | 12 | c | false | <90% | 10156 | ||
| NM_004270 | CRSP9 | 196 | 214 | g | U | U | U | g | G | C | A | A | U | C | A | g | U | U | C | C | A | A | 36 | 3 | 7 | false | <90% | 1066 | |||
| NM_152551 | C6orf151 | 2109 | 2127 | C | U | U | U | C | c | C | A | A | U | C | A | A | U | U | C | C | u | c | 29 | 3 | 11 | c | false | <90% | 4173 | ||
| NM_004905 | PRDX6 | 907 | 925 | C | U | U | c | a | G | C | A | A | U | C | A | A | U | U | C | C | A | u | 6 | 3 | 13 | bc | false | <90% | 1715 | ||
| NM_032793 | MFSD2 | 1127 | 1145 | C | U | U | c | C | G | C | A | A | U | g | A | A | U | U | C | C | A | g | -3 | 3 | 7 | c | false | <90% | 2170 | ||
| NR_002723 | GABPAP | 163415 | 163433 | C | U | U | U | C | a | g | A | A | U | C | A | A | U | U | C | C | A | c | -34 | 3 | 11 | bc | false | <90% | 194142 | ||
3 prime UTR Seed matches
Hits to same gene : 0
Hits to other genes : 3075
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