Automatic recommendation
OK - siRNA is specific for both sense and antisense (guide) strands
10 hits were found for GAUGUCACGGUAAAGAGCA (8 guide strand hits and 2 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_175907 | ZADH2 | 2807 | 2825 | a | A | U | G | U | C | A | C | G | G | U | A | A | A | u | A | G | C | u | 68 | 3 | 13 | c | false | <90% | 4132 | ||
| NM_173570 | ZDHHC23 | 3376 | 3394 | G | A | U | G | U | C | A | C | a | G | U | A | u | A | G | A | G | C | c | 24 | 3 | 8 | false | <90% | 3789 | |||
| NM_000301 | PLG | 248 | 266 | a | A | U | a | U | C | A | C | a | G | U | A | A | A | G | A | G | C | A | 1 | 3 | 10 | bc | false | <90% | 2732 | ||
| NM_001032392 | PLGLB1 | 257 | 275 | a | A | U | a | U | C | A | C | a | G | U | A | A | A | G | A | G | C | A | 1 | 3 | 10 | bc | false | <90% | 3011 | ||
| NM_002665 | PLGLB2 | 261 | 279 | a | A | U | a | U | C | A | C | a | G | U | A | A | A | G | A | G | C | A | 1 | 3 | 10 | bc | false | <90% | 3016 | ||
| NR_003506 | PLGLA1 | 16435 | 16453 | a | A | U | a | U | C | A | C | a | G | U | A | A | A | G | A | G | C | A | 1 | 3 | 10 | bc | false | <90% | 22167 | ||
| NM_014071 | NCOA6 | 2957 | 2975 | G | A | U | G | U | C | A | C | G | c | U | A | A | c | G | A | G | C | c | -7 | 3 | 9 | c | false | <90% | 7062 | ||
| NM_001017995 | SH3PXD2B | 6442 | 6460 | u | A | U | G | c | C | A | C | G | u | U | A | A | A | G | A | G | C | A | -36 | 3 | 9 | bc | false | <90% | 7777 | ||
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_005920 | MEF2D | 215 | 233 | c | G | C | U | C | U | U | U | g | C | C | G | U | G | A | C | A | a | C | 35 | 3 | 8 | c | false | <90% | 5888 | ||
| NM_017460 | CYP3A4 | 1299 | 1317 | U | G | C | U | C | U | U | c | A | C | C | G | U | G | A | C | c | c | a | 6 | 4 | 8 | c | false | <90% | 2768 | ||
3 prime UTR Seed matches
Hits to same gene : 0
Hits to other genes : 1859
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