Automatic recommendation
OK - siRNA is specific for both sense and antisense (guide) strands
14 hits were found for AGGCAUCUAAAAAGCCUCG (6 guide strand hits and 8 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_002841 | PTPRG | 2801 | 2819 | u | G | c | C | A | U | C | U | A | A | A | A | A | G | C | C | U | a | u | 70 | 4 | 14 | c | false | <90% | 5787 | ||
| NM_001001563 | TIMM50 | 1751 | 1769 | c | G | G | a | A | U | C | U | A | A | A | A | A | c | C | C | U | C | G | 41 | 3 | 9 | c | false | <90% | 2572 | ||
| NM_006720 | ABLIM1 | 160 | 178 | u | G | G | C | A | U | C | U | A | c | A | A | A | G | C | C | U | C | u | 10 | 3 | 8 | bc | false | <90% | 6850 | ||
| NM_003921 | BCL10 | 1910 | 1928 | A | G | G | C | A | U | g | U | A | A | A | c | A | G | C | C | U | C | u | -5 | 3 | 6 | false | <90% | 3271 | |||
| NM_000572 | IL10 | 515 | 533 | A | G | G | C | A | U | C | U | A | c | A | A | A | G | C | C | a | u | G | -8 | 3 | 9 | c | false | <90% | 1629 | ||
| NM_018301 | RBM41 | 101 | 119 | A | G | G | C | A | g | C | U | g | A | A | A | A | G | C | C | U | C | c | -28 | 3 | 9 | bc | false | <90% | 1689 | ||
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_014314 | DDX58 | 369 | 387 | C | G | u | G | G | C | U | U | U | U | U | g | G | A | U | G | C | C | c | 41 | 3 | 8 | false | <90% | 4759 | |||
| NM_002994 | CXCL5 | 2288 | 2306 | C | u | g | a | G | C | U | U | U | U | U | A | G | A | U | G | C | C | U | 32 | 3 | 15 | bc | false | <90% | 2475 | ||
| XM_931631 | ZC3H12C | 7540 | 7558 | u | u | A | G | G | a | U | U | U | U | U | A | G | A | U | G | C | C | U | 23 | 3 | 13 | bc | false | <90% | 8772 | ||
| XM_938482 | ZC3H12C | 8310 | 8328 | u | u | A | G | G | a | U | U | U | U | U | A | G | A | U | G | C | C | U | 23 | 3 | 13 | bc | false | <90% | 9542 | ||
| XM_370654 | ZC3H12C | 8310 | 8328 | u | u | A | G | G | a | U | U | U | U | U | A | G | A | U | G | C | C | U | 23 | 3 | 13 | bc | false | <90% | 9542 | ||
| NM_014596 | ZNRD1 | 589 | 607 | a | c | u | G | G | g | U | U | U | U | U | A | G | A | U | G | C | C | U | 3 | 4 | 13 | bc | false | <90% | 751 | ||
| NM_170783 | ZNRD1 | 705 | 723 | a | c | u | G | G | g | U | U | U | U | U | A | G | A | U | G | C | C | U | 3 | 4 | 13 | bc | false | <90% | 867 | ||
| NM_024996 | GFM1 | 1873 | 1891 | a | a | g | G | G | g | U | U | U | U | U | A | G | A | U | G | C | C | U | 3 | 4 | 13 | bc | false | <90% | 3468 | ||
3 prime UTR Seed matches
Hits to same gene : 0
Hits to other genes : 1552
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