Automatic recommendation
OK - siRNA is specific for both sense and antisense (guide) strands
17 hits were found for GGGGAGGAGAUUAGGUUAA (15 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_004586 | RPS6KA3 | 452 | 470 | G | G | G | G | A | G | G | A | G | A | U | U | u | G | u | U | U | A | c | 59 | 3 | 12 | false | <90% | 7723 | |||
| NM_006934 | SLC6A9 | 95 | 113 | c | G | G | G | A | G | G | A | G | A | U | g | A | G | G | U | g | A | A | 40 | 3 | 10 | false | <90% | 3213 | |||
| NM_201649 | SLC6A9 | 95 | 113 | c | G | G | G | A | G | G | A | G | A | U | g | A | G | G | U | g | A | A | 40 | 3 | 10 | false | <90% | 3375 | |||
| NM_018958 | C15orf2 | 6102 | 6120 | G | G | G | G | A | G | G | u | G | A | U | U | A | G | G | U | U | u | A | 35 | 2 | 9 | c | false | <90% | 8053 | ||
| XM_943661 | LRRC38 | 1737 | 1755 | u | G | G | G | A | G | G | u | G | A | U | U | A | G | G | U | U | u | A | 33 | 3 | 9 | c | false | <90% | 2235 | ||
| XM_059074 | LRRC38 | 1782 | 1800 | u | G | G | G | A | G | G | u | G | A | U | U | A | G | G | U | U | u | A | 33 | 3 | 9 | c | false | <90% | 2280 | ||
| NM_013358 | PADI1 | 3016 | 3034 | u | G | G | G | A | G | G | A | a | A | U | U | A | G | G | U | U | A | u | 32 | 3 | 9 | bc | false | <90% | 3847 | ||
| NM_015341 | NCAPH | 4344 | 4362 | u | G | G | G | A | G | G | u | G | A | U | U | A | G | G | U | U | A | u | 30 | 3 | 10 | bc | false | <90% | 4495 | ||
| NM_001040659 | TTC23 | 2938 | 2956 | G | G | a | G | A | G | G | u | G | A | U | U | A | G | G | U | U | A | u | 13 | 3 | 10 | bc | false | <90% | 3245 | ||
| NM_001040658 | TTC23 | 3060 | 3078 | G | G | a | G | A | G | G | u | G | A | U | U | A | G | G | U | U | A | u | 13 | 3 | 10 | bc | false | <90% | 3367 | ||
| NM_001040657 | TTC23 | 3133 | 3151 | G | G | a | G | A | G | G | u | G | A | U | U | A | G | G | U | U | A | u | 13 | 3 | 10 | bc | false | <90% | 3440 | ||
| NM_001040656 | TTC23 | 3184 | 3202 | G | G | a | G | A | G | G | u | G | A | U | U | A | G | G | U | U | A | u | 13 | 3 | 10 | bc | false | <90% | 3491 | ||
| NM_022905 | TTC23 | 3255 | 3273 | G | G | a | G | A | G | G | u | G | A | U | U | A | G | G | U | U | A | u | 13 | 3 | 10 | bc | false | <90% | 3562 | ||
| NM_001040660 | TTC23 | 3379 | 3397 | G | G | a | G | A | G | G | u | G | A | U | U | A | G | G | U | U | A | u | 13 | 3 | 10 | bc | false | <90% | 3686 | ||
| NM_001040655 | TTC23 | 3501 | 3519 | G | G | a | G | A | G | G | u | G | A | U | U | A | G | G | U | U | A | u | 13 | 3 | 10 | bc | false | <90% | 3808 | ||
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_001012755 | MCART6 | 5663 | 5681 | a | U | A | A | C | C | U | A | c | U | C | U | u | C | U | C | C | C | C | 27 | 3 | 7 | false | <90% | 6240 | |||
| NM_133489 | SLC26A10 | 1275 | 1293 | c | c | A | A | C | C | U | c | A | U | C | U | C | C | U | C | C | C | u | 19 | 4 | 10 | bc | false | <90% | 2446 | ||
3 prime UTR Seed matches
Hits to same gene : 0
Hits to other genes : 4463
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