Automatic recommendation
Warning - siRNA is specific for only the antisense (guide) strand
14 hits were found for ACACAACAUGGAACAAUAG (11 guide strand hits and 3 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_014648 | DZIP3 | 5108 | 5126 | c | C | A | C | A | A | C | A | U | G | G | A | A | u | A | A | U | g | G | 75 | 3 | 12 | c | false | <90% | 5319 | ||
| NM_032408 | BAZ1B | 3250 | 3268 | A | C | A | C | A | A | C | A | U | G | G | A | A | C | A | g | c | A | a | 45 | 3 | 15 | c | false | <90% | 6096 | ||
| NM_016351 | ADAM22 | 2916 | 2934 | c | u | A | u | A | A | C | A | U | G | G | A | A | C | A | A | U | A | a | 44 | 4 | 14 | bc | false | <90% | 3347 | ||
| NM_021722 | ADAM22 | 2962 | 2980 | c | u | A | u | A | A | C | A | U | G | G | A | A | C | A | A | U | A | a | 44 | 4 | 14 | bc | false | <90% | 3393 | ||
| NM_021723 | ADAM22 | 3024 | 3042 | c | u | A | u | A | A | C | A | U | G | G | A | A | C | A | A | U | A | a | 44 | 4 | 14 | bc | false | <90% | 3455 | ||
| XR_016401 | LOC392543 | 945 | 963 | u | C | A | C | A | A | C | A | c | G | G | A | A | C | A | A | U | c | a | 30 | 4 | 8 | c | false | <90% | 1267 | ||
| XR_018603 | LOC392543 | 945 | 963 | u | C | A | C | A | A | C | A | c | G | G | A | A | C | A | A | U | c | a | 30 | 4 | 8 | c | false | <90% | 1267 | ||
| NM_001040020 | FAM3C | 623 | 641 | A | u | A | C | A | A | g | A | U | G | G | A | A | C | A | A | U | A | G | 22 | 2 | 12 | bc | false | <90% | 2512 | ||
| NM_014888 | FAM3C | 663 | 681 | A | u | A | C | A | A | g | A | U | G | G | A | A | C | A | A | U | A | G | 22 | 2 | 12 | bc | false | <90% | 2552 | ||
| NM_021141 | XRCC5 | 385 | 403 | A | u | u | C | A | A | C | A | U | G | a | A | A | C | A | A | U | A | G | 7 | 3 | 8 | c | false | <90% | 3310 | ||
| NM_203454 | APOBEC4 | 300 | 318 | g | C | A | a | A | u | C | A | U | G | G | A | A | C | A | A | U | A | G | -2 | 3 | 13 | bc | false | <90% | 2786 | ||
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_032420 | PCDH1 | 4617 | 4635 | C | U | A | U | U | G | U | U | C | C | A | U | G | U | U | G | U | a | a | 92 | 2 | 17 | ac | false | <90% | 4779 | ||
| NM_020872 | CNTN3 | 4845 | 4863 | C | U | A | U | U | G | U | U | u | C | A | U | G | U | U | G | U | u | U | 37 | 2 | 8 | c | false | <90% | 4997 | ||
| NM_152641 | ARID2 | 7284 | 7302 | u | U | A | U | U | G | U | U | u | g | A | U | G | U | U | G | U | G | U | -44 | 3 | 9 | bc | false | <90% | 8466 | ||
3 prime UTR Seed matches
Hits to same gene : 0
Hits to other genes : 1291
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 sense 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