Automatic recommendation
Warning - siRNA is specific for only the antisense (guide) strand
10 hits were found for GAUCUCAAUCUCGGGAAUC (5 guide strand hits and 5 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_001025930 | TTLL3 | 541 | 559 | u | g | U | C | U | C | A | A | U | C | U | C | c | G | G | A | A | U | u | 71 | 4 | 10 | false | <90% | 3415 | |||
| NM_015644 | TTLL3 | 536 | 554 | u | g | U | C | U | C | A | A | U | C | U | C | c | G | G | A | A | U | u | 71 | 4 | 10 | false | <90% | 3454 | |||
| NM_152564 | VPS13B | 7264 | 7282 | G | A | U | a | U | C | A | A | U | C | U | C | G | u | G | A | A | U | g | 38 | 3 | 9 | c | false | <90% | 14036 | ||
| NM_017890 | VPS13B | 7339 | 7357 | G | A | U | a | U | C | A | A | U | C | U | C | G | u | G | A | A | U | g | 38 | 3 | 9 | c | false | <90% | 14111 | ||
| NM_014494 | TNRC6A | 5800 | 5818 | G | A | U | C | U | C | A | A | U | C | a | C | u | G | G | A | A | U | g | 23 | 3 | 10 | false | <90% | 8438 | |||
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_138769 | RHOT2 | 479 | 497 | G | u | U | U | C | C | C | G | A | G | A | U | U | G | A | G | A | c | C | 85 | 2 | 15 | ac | false | <90% | 2509 | ||
| NM_001005327 | OR6K3 | 516 | 534 | G | c | U | U | C | C | C | G | A | G | A | U | U | G | u | G | A | U | g | 58 | 3 | 12 | c | false | <90% | 996 | ||
| NM_001011885 | BTBD1 | 2329 | 2347 | G | A | U | U | C | C | C | a | A | G | A | U | U | G | A | G | A | U | g | 32 | 2 | 10 | bc | false | <90% | 3220 | ||
| NM_025238 | BTBD1 | 2417 | 2435 | G | A | U | U | C | C | C | a | A | G | A | U | U | G | A | G | A | U | g | 32 | 2 | 10 | bc | false | <90% | 3308 | ||
| NM_001389 | DSCAM | 3117 | 3135 | c | c | c | U | C | C | C | G | A | a | A | U | U | G | A | G | A | U | C | -15 | 4 | 9 | bc | false | <90% | 7110 | ||
3 prime UTR Seed matches
Hits to same gene : 0
Hits to other genes : 1683
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