Automatic recommendation
OK - siRNA is specific for both sense and antisense (guide) strands
11 hits were found for UUGUUCUCGAGGGCCUUCC (1 guide strand hits and 10 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_017877 | C2orf18 | 464 | 482 | c | U | G | U | U | C | U | C | G | g | u | G | G | C | C | U | U | C | C | -46 | 3 | 8 | c | false | <90% | 3912 | ||
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_006191 | PA2G4 | 171 | 189 | c | G | A | A | G | G | C | C | C | U | C | G | A | G | A | g | C | g | g | 64 | 4 | 14 | c | false | <90% | 2643 | ||
| NM_030792 | GDPD5 | 1505 | 1523 | G | G | A | A | G | G | C | C | C | U | C | G | A | G | c | A | g | A | A | 51 | 2 | 14 | c | false | <90% | 3500 | ||
| NM_018964 | SLC37A1 | 47 | 65 | G | G | A | A | G | G | C | C | C | U | C | G | A | G | A | g | a | g | u | 42 | 4 | 15 | c | false | <90% | 3098 | ||
| NM_145701 | CDCA4 | 607 | 625 | G | G | A | u | G | G | C | C | C | U | C | G | A | G | A | A | a | A | c | 34 | 3 | 12 | c | false | <90% | 1645 | ||
| NM_017955 | CDCA4 | 607 | 625 | G | G | A | u | G | G | C | C | C | U | C | G | A | G | A | A | a | A | c | 34 | 3 | 12 | c | false | <90% | 2171 | ||
| NM_032526 | NT5C1A | 712 | 730 | a | G | A | A | G | G | C | C | C | a | C | G | A | G | A | A | C | A | A | 15 | 2 | 9 | bc | false | <90% | 1107 | ||
| NM_003086 | SNAPC4 | 3973 | 3991 | a | G | A | A | G | G | C | C | C | U | g | G | A | G | c | A | C | A | A | 11 | 3 | 9 | c | false | <90% | 4661 | ||
| NM_018025 | GPATCH1 | 2059 | 2077 | u | G | A | A | G | u | C | C | C | U | C | G | A | G | A | c | C | A | A | 8 | 3 | 9 | c | false | <90% | 3390 | ||
| NM_007353 | GNA12 | 558 | 576 | u | G | A | u | G | G | C | C | u | U | C | G | A | G | A | A | C | A | A | 1 | 3 | 10 | bc | false | <90% | 4398 | ||
| NM_015124 | DIP | 2612 | 2630 | G | G | A | A | G | G | C | C | C | a | g | G | A | G | A | A | C | A | u | -49 | 3 | 9 | c | false | <90% | 4316 | ||
3 prime UTR Seed matches
Hits to same gene : 0
Hits to other genes : 3905
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