Automatic recommendation
OK - siRNA is specific for both sense and antisense (guide) strands
12 hits were found for UACAGACAUGGUGCGAAGA (8 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_018066 | ATPBD1B | 1373 | 1391 | g | c | C | A | G | A | C | A | U | G | G | U | G | C | c | A | A | G | c | 56 | 4 | 12 | c | false | <90% | 1510 | ||
| XR_016968 | LOC400011 | 944 | 962 | U | u | a | A | G | A | C | A | U | G | G | U | G | u | G | A | A | G | A | 49 | 3 | 10 | c | false | <90% | 3628 | ||
| XR_019334 | LOC400011 | 944 | 962 | U | u | a | A | G | A | C | A | U | G | G | U | G | u | G | A | A | G | A | 49 | 3 | 10 | c | false | <90% | 3628 | ||
| NM_007192 | SUPT16H | 1285 | 1303 | U | u | a | A | G | A | C | A | U | G | G | U | G | u | G | A | A | G | A | 49 | 3 | 10 | c | false | <90% | 4696 | ||
| NM_004273 | CHST3 | 6400 | 6418 | U | A | C | A | G | A | C | A | U | G | G | U | G | C | c | A | u | c | c | 44 | 4 | 14 | c | false | <90% | 6961 | ||
| NM_203467 | PPIL5 | 166 | 184 | U | A | C | A | G | A | C | A | c | G | G | U | G | C | u | A | A | G | A | 15 | 2 | 8 | c | false | <90% | 1049 | ||
| NM_152329 | PPIL5 | 166 | 184 | U | A | C | A | G | A | C | A | c | G | G | U | G | C | u | A | A | G | A | 15 | 2 | 8 | c | false | <90% | 1760 | ||
| NM_001034955 | SORBS1 | 2972 | 2990 | c | A | C | A | G | c | C | A | U | G | G | c | G | C | G | A | A | G | A | 0 | 3 | 7 | false | <90% | 6803 | |||
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_148919 | PSMB8 | 382 | 400 | g | C | U | U | g | G | C | A | C | C | A | U | G | U | C | U | G | g | c | 38 | 4 | 12 | c | false | <90% | 1135 | ||
| NM_004159 | PSMB8 | 849 | 867 | g | C | U | U | g | G | C | A | C | C | A | U | G | U | C | U | G | g | c | 38 | 4 | 12 | c | false | <90% | 1602 | ||
| NM_178831 | GATS | 869 | 887 | U | C | U | a | C | u | C | A | C | C | A | U | G | U | C | U | G | U | A | 0 | 2 | 13 | bc | false | <90% | 3493 | ||
| NR_001558 | C20orf56 | 8481 | 8499 | U | C | U | U | u | G | C | A | C | a | A | U | G | U | C | U | G | U | c | -39 | 3 | 8 | bc | false | <90% | 18090 | ||
3 prime UTR Seed matches
Hits to same gene : 0
Hits to other genes : 1499
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