Automatic recommendation
OK - siRNA is specific for both sense and antisense (guide) strands
17 hits were found for GAUGAAUUGCUUGACGCUG (5 guide strand hits and 12 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_018482 | DDEF1 | 1721 | 1739 | a | A | U | G | A | A | U | U | G | C | U | U | G | A | g | G | C | c | a | 65 | 4 | 13 | c | false | <90% | 6042 | ||
| NM_174911 | FAM84B | 3558 | 3576 | G | A | a | G | A | A | U | U | G | C | U | U | G | A | a | G | C | U | G | 55 | 2 | 11 | c | false | <90% | 5249 | ||
| NM_004279 | PMPCB | 782 | 800 | G | A | U | G | A | A | U | U | G | C | U | U | G | A | C | u | u | a | G | 47 | 3 | 15 | c | false | <90% | 3939 | ||
| NM_080876 | DUSP19 | 5079 | 5097 | G | g | a | G | A | A | U | U | G | C | U | U | G | A | C | c | C | U | G | 42 | 3 | 12 | c | false | <90% | 5183 | ||
| NM_003629 | PIK3R3 | 4462 | 4480 | c | A | U | G | A | c | U | U | G | C | U | U | G | A | C | c | C | U | G | 8 | 3 | 9 | c | false | <90% | 5621 | ||
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_005548 | KARS | 283 | 301 | C | g | c | a | G | U | C | A | A | G | C | A | A | U | U | C | A | U | C | 32 | 3 | 15 | bc | false | <90% | 1997 | ||
| NM_013291 | CPSF1 | 3724 | 3742 | C | A | G | C | G | U | C | A | A | G | a | A | c | U | U | C | A | U | C | 28 | 2 | 10 | false | <90% | 4494 | |||
| NM_178564 | NRBP2 | 271 | 289 | C | A | G | C | c | U | C | A | A | G | C | A | A | U | U | C | c | U | C | 25 | 2 | 11 | c | false | <90% | 3538 | ||
| NM_003298 | NR2C2 | 490 | 508 | C | A | G | C | G | c | C | A | A | G | C | A | A | c | U | C | A | U | a | 12 | 3 | 7 | c | false | <90% | 8330 | ||
| NM_024656 | GLT25D1 | 2438 | 2456 | C | A | G | C | G | U | C | c | A | G | C | A | A | U | U | C | u | U | g | 9 | 3 | 8 | c | false | <90% | 3593 | ||
| XR_018548 | LOC649059 | 1233 | 1251 | C | A | G | C | G | U | C | A | g | G | C | A | A | U | U | C | c | c | u | 8 | 4 | 8 | c | false | <90% | 2584 | ||
| XR_016505 | LOC400036 | 1234 | 1252 | C | A | G | C | G | U | C | A | g | G | C | A | A | U | U | C | c | c | u | 8 | 4 | 8 | c | false | <90% | 2585 | ||
| NM_004818 | DDX23 | 1341 | 1359 | C | A | G | C | G | U | C | A | g | G | C | A | A | U | U | C | c | c | a | 8 | 4 | 8 | c | false | <90% | 3288 | ||
| XM_001132149 | LOC732189 | 644 | 662 | a | A | c | u | c | U | C | A | A | G | C | A | A | U | U | C | A | U | C | -9 | 4 | 14 | bc | false | <90% | 715 | ||
| XM_001133046 | LOC730226 | 644 | 662 | a | A | c | u | c | U | C | A | A | G | C | A | A | U | U | C | A | U | C | -9 | 4 | 14 | bc | false | <90% | 715 | ||
| XM_496575 | FLJ14082 | 1341 | 1359 | C | A | G | C | G | U | g | g | A | G | C | A | A | U | U | C | A | U | C | -28 | 2 | 11 | bc | false | <90% | 3560 | ||
| XM_936846 | FLJ14082 | 1341 | 1359 | C | A | G | C | G | U | g | g | A | G | C | A | A | U | U | C | A | U | C | -28 | 2 | 11 | bc | false | <90% | 3560 | ||
3 prime UTR Seed matches
Hits to same gene : 0
Hits to other genes : 2071
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