Automatic recommendation
OK - siRNA is specific for both sense and antisense (guide) strands
8 hits were found for GCCUGAGAUUAUCGUGGAG (3 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_001038633 | RSPO1 | 642 | 660 | a | g | C | U | G | A | G | A | U | U | A | U | g | G | U | G | G | A | u | 71 | 4 | 10 | false | <90% | 2995 | |||
| NM_000292 | PHKA2 | 1731 | 1749 | c | a | a | U | G | A | G | A | U | g | A | U | C | G | U | G | G | A | G | -15 | 4 | 9 | bc | false | <90% | 4566 | ||
| NM_003260 | TLE2 | 708 | 726 | c | C | C | U | G | A | G | A | g | U | c | U | C | G | U | G | G | A | G | -23 | 3 | 8 | c | false | <90% | 2579 | ||
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_021733 | TSKS | 1679 | 1697 | C | U | C | C | A | C | G | A | U | c | A | U | C | U | C | A | G | c | a | 9 | 3 | 9 | c | false | <90% | 1812 | ||
| XR_019621 | LOC346702 | 828 | 846 | C | U | a | C | A | C | c | A | U | A | A | U | C | U | C | A | G | G | a | 9 | 3 | 11 | bc | false | <90% | 962 | ||
| NM_001527 | HDAC2 | 5650 | 5668 | C | U | C | C | A | C | c | A | U | A | A | U | C | U | u | A | G | G | a | 4 | 3 | 7 | c | false | <90% | 6659 | ||
| NM_032237 | FLJ23356 | 1059 | 1077 | u | U | C | C | A | C | G | A | U | g | A | U | C | U | C | A | u | G | C | -8 | 3 | 8 | c | false | <90% | 1612 | ||
| NM_032855 | HSH2D | 1247 | 1265 | a | U | C | C | A | C | G | g | U | g | A | U | C | U | C | A | G | G | C | -46 | 3 | 9 | bc | false | <90% | 2369 | ||
3 prime UTR Seed matches
Hits to same gene : 0
Hits to other genes : 2826
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