Automatic recommendation
OK - siRNA is specific for both sense and antisense (guide) strands
12 hits were found for GCCCCCGAUUGGGGGCGAC (9 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_033113 | ZNF628 | 457 | 475 | u | C | C | C | C | C | G | A | U | U | G | G | G | G | c | C | G | c | a | 65 | 4 | 13 | c | false | <90% | 3864 | ||
| XM_940069 | PPP1R3E | 953 | 971 | G | C | C | g | C | C | G | A | U | U | G | G | G | G | G | C | G | c | C | 60 | 2 | 13 | c | false | <90% | 6563 | ||
| XM_927029 | PPP1R3E | 953 | 971 | G | C | C | g | C | C | G | A | U | U | G | G | G | G | G | C | G | c | C | 60 | 2 | 13 | c | false | <90% | 6564 | ||
| NM_015062 | PPRC1 | 78 | 96 | G | C | C | C | C | C | G | A | g | U | G | G | G | G | G | C | c | c | C | 13 | 3 | 8 | c | false | <90% | 5354 | ||
| NM_172337 | OTX2 | 129 | 147 | a | C | C | C | C | C | G | A | U | U | u | G | G | G | c | C | G | A | C | 11 | 3 | 9 | c | false | <90% | 2082 | ||
| NM_021728 | OTX2 | 232 | 250 | a | C | C | C | C | C | G | A | U | U | u | G | G | G | c | C | G | A | C | 11 | 3 | 9 | c | false | <90% | 2209 | ||
| XM_001134465 | OTUD1 | 1262 | 1280 | c | C | C | C | C | u | G | A | U | U | G | a | G | G | G | C | G | A | C | 0 | 3 | 7 | false | <90% | 3121 | |||
| XM_166659 | OTUD1 | 1653 | 1671 | c | C | C | C | C | u | G | A | U | U | G | a | G | G | G | C | G | A | C | 0 | 3 | 7 | false | <90% | 3512 | |||
| NM_014726 | TBKBP1 | 936 | 954 | c | C | C | C | u | C | G | c | U | U | G | G | G | G | G | C | G | A | C | -15 | 3 | 11 | bc | false | <90% | 4121 | ||
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_001538 | HSF4 | 2348 | 2366 | G | g | C | G | C | C | C | C | C | u | A | U | C | G | G | G | G | G | u | 0 | 3 | 8 | bc | false | <90% | 2445 | ||
| NM_001040667 | HSF4 | 2438 | 2456 | G | g | C | G | C | C | C | C | C | u | A | U | C | G | G | G | G | G | u | 0 | 3 | 8 | bc | false | <90% | 2535 | ||
| NM_001012279 | C6orf174 | 98 | 116 | u | c | a | G | C | C | a | C | C | A | A | U | C | G | G | G | G | G | C | 0 | 4 | 12 | bc | false | <90% | 3556 | ||
3 prime UTR Seed matches
Hits to same gene : 0
Hits to other genes : 1086
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