Automatic recommendation
OK - siRNA is specific for both sense and antisense (guide) strands
15 hits were found for GUGUCUCUUGUCUAUGUCA (8 guide strand hits and 7 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_020652 | ZNF286A | 2185 | 2203 | c | c | c | U | C | U | C | U | U | G | U | u | U | A | U | G | U | C | A | 33 | 4 | 8 | false | <90% | 2515 | |||
| NM_031476 | CRISPLD2 | 2401 | 2419 | a | U | G | U | a | U | C | U | U | G | U | C | U | u | U | G | U | C | A | 27 | 3 | 8 | c | false | <90% | 4572 | ||
| XM_939510 | DUB3 | 685 | 703 | G | g | a | c | C | U | C | U | U | G | U | C | U | A | U | G | U | C | c | 27 | 4 | 14 | bc | false | <90% | 945 | ||
| XR_017907 | DUB4 | 937 | 955 | G | g | a | c | C | U | C | U | U | G | U | C | U | A | U | G | U | C | c | 27 | 4 | 14 | bc | false | <90% | 1197 | ||
| XR_018634 | LOC649346 | 937 | 955 | G | g | a | c | C | U | C | U | U | G | U | C | U | A | U | G | U | C | c | 27 | 4 | 14 | bc | false | <90% | 1214 | ||
| NM_002899 | RBP1 | 649 | 667 | c | U | G | U | C | U | C | U | U | G | g | C | U | u | U | G | U | C | A | 17 | 3 | 9 | c | false | <90% | 720 | ||
| NM_033518 | SLC38A5 | 221 | 239 | G | U | G | U | C | U | C | c | U | G | U | C | U | A | U | G | a | C | u | 9 | 3 | 8 | c | false | <90% | 2667 | ||
| NM_006778 | TRIM10 | 1373 | 1391 | G | U | G | U | C | U | C | U | U | G | a | C | U | A | U | G | a | g | g | 7 | 4 | 10 | c | false | <90% | 2004 | ||
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_005013 | NUCB2 | 326 | 344 | U | G | A | C | A | U | A | G | A | C | A | A | G | A | c | A | a | A | a | 46 | 3 | 14 | c | false | <90% | 1612 | ||
| NM_021736 | CLCN6 | 730 | 748 | c | G | A | C | A | g | A | G | A | C | A | A | G | A | G | A | g | A | C | 11 | 3 | 10 | c | false | <90% | 3993 | ||
| NM_001286 | CLCN6 | 730 | 748 | c | G | A | C | A | g | A | G | A | C | A | A | G | A | G | A | g | A | C | 11 | 3 | 10 | c | false | <90% | 5541 | ||
| NM_006567 | FARS2 | 1008 | 1026 | g | c | g | C | A | U | A | a | A | C | A | A | G | A | G | A | C | A | C | 4 | 4 | 11 | bc | false | <90% | 1841 | ||
| NM_181492 | TCF20 | 4343 | 4361 | U | G | A | C | A | U | A | G | A | g | A | A | G | A | G | A | a | A | a | -11 | 3 | 9 | c | false | <90% | 7279 | ||
| NM_005650 | TCF20 | 4343 | 4361 | U | G | A | C | A | U | A | G | A | g | A | A | G | A | G | A | a | A | a | -11 | 3 | 9 | c | false | <90% | 7407 | ||
| NM_001429 | EP300 | 7637 | 7655 | a | G | A | C | A | U | A | c | A | C | u | A | G | A | G | A | C | A | C | -25 | 3 | 8 | c | false | <90% | 8765 | ||
3 prime UTR Seed matches
Hits to same gene : 0
Hits to other genes : 2058
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