Automatic recommendation
OK - siRNA is specific for both sense and antisense (guide) strands
14 hits were found for GCAUUUGACUACACAGGUU (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_015600 | ABHD12 | 742 | 760 | a | C | c | U | U | U | G | A | C | U | A | C | A | g | A | G | G | U | U | 58 | 3 | 10 | c | false | <90% | 1610 | ||
| NM_001042472 | ABHD12 | 742 | 760 | a | C | c | U | U | U | G | A | C | U | A | C | A | g | A | G | G | U | U | 58 | 3 | 10 | c | false | <90% | 1983 | ||
| NM_001004360 | DPP10 | 2594 | 2612 | G | C | A | U | U | U | G | A | a | U | A | C | A | C | A | a | G | U | c | 8 | 3 | 8 | c | false | <90% | 4464 | ||
| NM_020868 | DPP10 | 2993 | 3011 | G | C | A | U | U | U | G | A | a | U | A | C | A | C | A | a | G | U | c | 8 | 3 | 8 | c | false | <90% | 4863 | ||
| NM_012420 | IFIT5 | 1129 | 1147 | G | C | A | U | U | U | G | c | C | U | A | C | A | C | A | G | a | c | c | 6 | 4 | 8 | c | false | <90% | 3906 | ||
| NM_006561 | CUGBP2 | 5968 | 5986 | u | C | u | U | U | U | G | A | C | c | A | C | A | C | A | G | G | U | U | -4 | 3 | 9 | bc | false | <90% | 8005 | ||
| NM_001083591 | CUGBP2 | 6016 | 6034 | u | C | u | U | U | U | G | A | C | c | A | C | A | C | A | G | G | U | U | -4 | 3 | 9 | bc | false | <90% | 8053 | ||
| NM_001025076 | CUGBP2 | 6022 | 6040 | u | C | u | U | U | U | G | A | C | c | A | C | A | C | A | G | G | U | U | -4 | 3 | 9 | bc | false | <90% | 8059 | ||
| NM_001025077 | CUGBP2 | 7219 | 7237 | u | C | u | U | U | U | G | A | C | c | A | C | A | C | A | G | G | U | U | -4 | 3 | 9 | bc | false | <90% | 9256 | ||
| XR_015396 | LOC728853 | 56 | 74 | G | C | A | g | U | U | G | A | C | c | A | C | A | C | A | G | G | U | a | -24 | 3 | 8 | bc | false | <90% | 3334 | ||
| XR_015633 | LOC731867 | 56 | 74 | G | C | A | g | U | U | G | A | C | c | A | C | A | C | A | G | G | U | a | -24 | 3 | 8 | bc | false | <90% | 3334 | ||
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 | |||||||||||||
| XM_940123 | LOC643475 | 2509 | 2527 | g | u | C | C | U | G | U | G | U | A | G | U | g | A | A | A | U | G | a | 71 | 4 | 10 | false | <90% | 4902 | |||
| XM_928745 | LOC643475 | 2509 | 2527 | g | u | C | C | U | G | U | G | U | A | G | U | g | A | A | A | U | G | a | 71 | 4 | 10 | false | <90% | 4904 | |||
| NM_000399 | EGR2 | 2806 | 2824 | u | A | C | C | U | u | U | G | U | A | G | U | C | A | A | A | U | u | u | 27 | 4 | 11 | c | false | <90% | 2984 | ||
3 prime UTR Seed matches
Hits to same gene : 0
Hits to other genes : 2897
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