Automatic recommendation
OK - siRNA is specific for both sense and antisense (guide) strands
13 hits were found for GUUUGCCAUAAAGCCAGGU (4 guide strand hits and 9 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_175727 | IL5RA | 1700 | 1718 | a | U | U | U | G | C | C | A | U | g | A | A | G | C | C | A | G | u | g | 7 | 4 | 8 | c | false | <90% | 1956 | ||
| NM_175724 | IL5RA | 1768 | 1786 | a | U | U | U | G | C | C | A | U | g | A | A | G | C | C | A | G | u | g | 7 | 4 | 8 | c | false | <90% | 2024 | ||
| NM_000285 | PEPD | 967 | 985 | G | g | g | U | G | C | C | A | U | g | A | A | G | C | C | A | G | G | U | -13 | 3 | 9 | bc | false | <90% | 1888 | ||
| NM_014149 | HSPC049 | 2747 | 2765 | c | U | U | U | G | C | C | A | U | g | g | A | G | C | C | A | G | G | U | -46 | 3 | 8 | c | false | <90% | 3179 | ||
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_006675 | TSPAN9 | 4245 | 4263 | u | C | C | U | G | G | C | U | U | U | A | U | G | G | a | A | c | A | C | 49 | 3 | 13 | c | false | <90% | 4338 | ||
| NM_020839 | WDR48 | 2757 | 2775 | u | C | C | U | G | G | C | U | U | U | g | U | G | G | C | A | A | c | C | 34 | 3 | 9 | c | false | <90% | 3705 | ||
| NM_001033520 | WIPI2 | 2806 | 2824 | g | g | u | U | G | G | C | U | U | U | A | c | G | G | C | A | A | A | C | 33 | 4 | 8 | false | <90% | 4295 | |||
| NM_001033519 | WIPI2 | 2913 | 2931 | g | g | u | U | G | G | C | U | U | U | A | c | G | G | C | A | A | A | C | 33 | 4 | 8 | false | <90% | 4402 | |||
| NM_016003 | WIPI2 | 2946 | 2964 | g | g | u | U | G | G | C | U | U | U | A | c | G | G | C | A | A | A | C | 33 | 4 | 8 | false | <90% | 4435 | |||
| NM_001033518 | WIPI2 | 2967 | 2985 | g | g | u | U | G | G | C | U | U | U | A | c | G | G | C | A | A | A | C | 33 | 4 | 8 | false | <90% | 4456 | |||
| NM_015610 | WIPI2 | 3000 | 3018 | g | g | u | U | G | G | C | U | U | U | A | c | G | G | C | A | A | A | C | 33 | 4 | 8 | false | <90% | 4489 | |||
| NM_032888 | COL27A1 | 4689 | 4707 | A | C | C | U | G | G | C | U | U | g | A | U | G | G | g | A | A | A | g | -12 | 3 | 9 | c | false | <90% | 5583 | ||
| NM_144490 | AKAP11 | 5275 | 5293 | A | C | C | U | G | G | C | U | U | g | A | U | G | G | C | A | u | u | u | -13 | 4 | 9 | c | false | <90% | 5947 | ||
3 prime UTR Seed matches
Hits to same gene : 0
Hits to other genes : 1688
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