Automatic recommendation
OK - siRNA is specific for both sense and antisense (guide) strands
16 hits were found for GACAUUAUUCAGACUCUGU (10 guide strand hits and 6 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_152761 | CXorf58 | 1009 | 1027 | u | u | C | A | U | U | A | U | U | C | A | G | A | g | U | C | U | G | g | 62 | 4 | 11 | c | false | <90% | 1547 | ||
| NM_152415 | VPS37A | 614 | 632 | a | A | a | A | U | U | A | U | U | C | A | G | A | g | U | C | U | G | U | 58 | 3 | 10 | c | false | <90% | 2020 | ||
| NM_014258 | SYCP2 | 464 | 482 | G | A | C | A | U | U | A | U | U | C | A | G | A | g | U | C | a | a | g | 49 | 4 | 13 | c | false | <90% | 5497 | ||
| NM_000770 | CYP2C8 | 1747 | 1765 | G | c | a | A | U | U | A | U | U | C | A | u | A | C | U | C | U | G | U | 35 | 3 | 8 | false | <90% | 1924 | |||
| NM_194285 | SPTY2D1 | 4145 | 4163 | u | u | C | A | g | U | A | U | U | C | A | G | A | C | U | C | U | G | a | 30 | 4 | 13 | bc | false | <90% | 5752 | ||
| NM_015971 | MRPS7 | 520 | 538 | c | u | C | A | U | g | A | U | U | C | A | G | A | C | U | C | U | G | g | 18 | 4 | 12 | bc | false | <90% | 1393 | ||
| XM_939581 | LOC344875 | 296 | 314 | a | g | u | A | U | U | c | U | U | C | A | G | A | C | U | C | U | G | U | 0 | 4 | 12 | bc | false | <90% | 3475 | ||
| XM_497913 | LOC344875 | 296 | 314 | a | g | u | A | U | U | c | U | U | C | A | G | A | C | U | C | U | G | U | 0 | 4 | 12 | bc | false | <90% | 3475 | ||
| XM_945019 | LOC643441 | 1763 | 1781 | u | A | C | A | U | U | c | U | c | C | A | G | A | C | U | C | U | G | U | -28 | 3 | 10 | bc | false | <90% | 2071 | ||
| XM_933124 | LOC643441 | 1763 | 1781 | u | A | C | A | U | U | c | U | c | C | A | G | A | C | U | C | U | G | U | -28 | 3 | 10 | bc | false | <90% | 2071 | ||
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_152573 | RASEF | 1200 | 1218 | u | C | A | G | A | G | U | C | U | G | A | A | U | A | c | U | G | a | a | 65 | 4 | 13 | c | false | <90% | 2770 | ||
| XM_045911 | STXBP5L | 4562 | 4580 | c | a | A | G | A | G | U | C | U | G | A | u | U | A | A | U | G | U | u | 47 | 4 | 9 | false | <90% | 5179 | |||
| XM_938898 | STXBP5L | 4562 | 4580 | c | a | A | G | A | G | U | C | U | G | A | u | U | A | A | U | G | U | u | 47 | 4 | 9 | false | <90% | 5179 | |||
| NM_181702 | GEM | 138 | 156 | g | a | u | G | A | c | U | C | U | G | A | A | U | A | A | U | G | U | C | 3 | 4 | 13 | bc | false | <90% | 2090 | ||
| NM_005261 | GEM | 253 | 271 | g | a | u | G | A | c | U | C | U | G | A | A | U | A | A | U | G | U | C | 3 | 4 | 13 | bc | false | <90% | 2205 | ||
| NM_003020 | SCG5 | 591 | 609 | A | C | A | G | A | G | a | C | U | G | g | A | U | A | A | U | G | U | u | -32 | 3 | 7 | c | false | <90% | 1151 | ||
3 prime UTR Seed matches
Hits to same gene : 0
Hits to other genes : 1454
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