Automatic recommendation
OK - siRNA is specific for both sense and antisense (guide) strands
12 hits were found for UUCACCUCUGCCUAAUCAU (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_006373 | VAT1 | 1636 | 1654 | U | U | C | A | C | C | U | C | U | G | C | C | U | c | A | U | C | u | U | 77 | 2 | 13 | c | false | <90% | 2758 | ||
| NM_016530 | RAB8B | 1380 | 1398 | a | U | u | A | C | C | U | C | U | G | C | C | U | A | A | U | C | u | a | 70 | 4 | 14 | c | false | <90% | 4877 | ||
| XR_016664 | LOC347281 | 1242 | 1260 | U | U | C | A | C | C | U | C | U | G | C | C | U | A | A | g | g | A | U | 50 | 2 | 15 | c | false | <90% | 2606 | ||
| XR_019067 | LOC347281 | 1242 | 1260 | U | U | C | A | C | C | U | C | U | G | C | C | U | A | A | g | g | A | U | 50 | 2 | 15 | c | false | <90% | 2606 | ||
| NM_007271 | STK38 | 765 | 783 | U | a | a | A | C | C | U | C | U | a | C | C | U | A | A | U | C | A | U | -13 | 3 | 9 | bc | false | <90% | 3593 | ||
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_001033520 | WIPI2 | 2903 | 2921 | u | g | c | A | U | U | A | G | G | C | A | G | A | G | G | U | G | c | A | 64 | 4 | 14 | c | false | <90% | 4295 | ||
| NM_001033519 | WIPI2 | 3010 | 3028 | u | g | c | A | U | U | A | G | G | C | A | G | A | G | G | U | G | c | A | 64 | 4 | 14 | c | false | <90% | 4402 | ||
| NM_016003 | WIPI2 | 3043 | 3061 | u | g | c | A | U | U | A | G | G | C | A | G | A | G | G | U | G | c | A | 64 | 4 | 14 | c | false | <90% | 4435 | ||
| NM_001033518 | WIPI2 | 3064 | 3082 | u | g | c | A | U | U | A | G | G | C | A | G | A | G | G | U | G | c | A | 64 | 4 | 14 | c | false | <90% | 4456 | ||
| NM_015610 | WIPI2 | 3097 | 3115 | u | g | c | A | U | U | A | G | G | C | A | G | A | G | G | U | G | c | A | 64 | 4 | 14 | c | false | <90% | 4489 | ||
| NM_006281 | STK3 | 1719 | 1737 | A | c | a | A | U | U | A | G | G | C | A | G | A | G | G | U | c | A | A | 45 | 3 | 13 | c | false | <90% | 2826 | ||
| NM_006736 | DNAJB2 | 1988 | 2006 | A | g | G | A | c | U | A | G | G | C | A | G | A | G | G | U | G | A | g | 32 | 3 | 13 | bc | false | <90% | 3129 | ||
3 prime UTR Seed matches
Hits to same gene : 0
Hits to other genes : 2563
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