Automatic recommendation
OK - siRNA is specific for both sense and antisense (guide) strands
15 hits were found for UGUGUGUACUGCAAGCAAC (14 guide strand hits and 1 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_001379 | DNMT1 | 1468 | 1486 | a | G | U | G | U | G | U | A | C | U | G | u | A | A | G | C | A | c | g | 56 | 4 | 10 | false | <90% | 5434 | |||
| NM_020861 | ZBTB2 | 2576 | 2594 | U | G | U | G | U | G | U | A | C | U | G | C | A | g | G | g | A | A | a | 49 | 3 | 13 | c | false | <90% | 3105 | ||
| NM_001040167 | LFNG | 1292 | 1310 | U | G | U | G | U | G | U | A | C | U | G | C | A | u | G | C | c | c | a | 49 | 4 | 13 | c | false | <90% | 2384 | ||
| NR_002771 | DLEU2L | 346 | 364 | a | a | g | G | U | G | U | A | C | U | G | C | A | A | G | g | A | A | C | 40 | 4 | 12 | c | false | <90% | 1657 | ||
| NR_002612 | DLEU2 | 433 | 451 | a | a | g | G | U | G | U | A | C | U | G | C | A | A | G | g | A | A | C | 40 | 4 | 12 | c | false | <90% | 2768 | ||
| NM_000693 | ALDH1A3 | 1973 | 1991 | U | G | U | G | U | G | U | u | C | U | G | C | A | A | G | C | A | g | g | 30 | 3 | 9 | c | false | <90% | 3442 | ||
| NM_032578 | MYPN | 2026 | 2044 | c | a | c | a | U | G | U | A | C | U | G | C | A | A | G | C | A | A | C | 30 | 4 | 15 | bc | false | <90% | 5707 | ||
| NM_003411 | ZFY | 2613 | 2631 | U | G | U | G | a | G | U | A | C | U | G | C | A | A | G | a | A | A | g | 17 | 3 | 10 | c | false | <90% | 4556 | ||
| NM_003410 | ZFX | 2590 | 2608 | U | G | U | G | a | G | U | A | C | U | G | C | A | A | G | a | A | A | g | 17 | 3 | 10 | c | false | <90% | 5811 | ||
| NM_001042729 | FGR | 219 | 237 | U | G | U | G | U | G | U | u | C | U | G | C | A | A | G | a | A | A | u | 6 | 3 | 7 | c | false | <90% | 2442 | ||
| NM_005248 | FGR | 235 | 253 | U | G | U | G | U | G | U | u | C | U | G | C | A | A | G | a | A | A | u | 6 | 3 | 7 | c | false | <90% | 2458 | ||
| NM_001042747 | FGR | 278 | 296 | U | G | U | G | U | G | U | u | C | U | G | C | A | A | G | a | A | A | u | 6 | 3 | 7 | c | false | <90% | 2501 | ||
| XR_019071 | LOC642333 | 2030 | 2048 | U | G | U | G | U | G | U | A | a | U | G | u | A | A | G | C | A | A | a | 1 | 3 | 8 | false | <90% | 2393 | |||
| XR_015164 | LOC727815 | 2043 | 2061 | U | G | U | G | U | G | U | A | a | U | G | u | A | A | G | C | A | A | a | 1 | 3 | 8 | false | <90% | 2406 | |||
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_015190 | DNAJC9 | 526 | 544 | u | U | U | G | C | g | U | G | C | A | G | U | A | C | A | C | A | g | A | 32 | 3 | 11 | c | false | <90% | 1450 | ||
3 prime UTR Seed matches
Hits to same gene : 0
Hits to other genes : 5156
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)
Motif found in guide strand
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