Automatic recommendation
OK - siRNA is specific for both sense and antisense (guide) strands
16 hits were found for GUUAUAUGGAUGAUGUGGU (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_153742 | CTH | 467 | 485 | u | U | U | g | U | A | U | G | G | A | U | G | A | U | G | U | G | u | a | 53 | 4 | 13 | c | false | <90% | 1687 | ||
| NM_001902 | CTH | 467 | 485 | u | U | U | g | U | A | U | G | G | A | U | G | A | U | G | U | G | u | a | 53 | 4 | 13 | c | false | <90% | 1819 | ||
| NM_006529 | GLRA3 | 1612 | 1630 | c | a | g | A | U | A | U | G | G | A | U | G | A | U | G | a | G | G | U | 40 | 4 | 12 | c | false | <90% | 3637 | ||
| NM_004654 | USP9Y | 9122 | 9140 | a | U | U | A | U | A | U | G | G | u | U | G | A | U | G | U | G | G | a | 10 | 3 | 8 | bc | false | <90% | 10048 | ||
| NM_020964 | KIAA1632 | 5865 | 5883 | c | U | U | A | U | A | U | G | G | c | U | G | A | U | G | U | G | a | a | 7 | 4 | 8 | c | false | <90% | 12715 | ||
| NM_001007248 | ZNF599 | 1084 | 1102 | G | U | U | A | U | A | U | G | G | c | U | G | A | U | G | U | c | a | U | -8 | 3 | 9 | c | false | <90% | 3101 | ||
| NM_001007247 | ZNF599 | 1214 | 1232 | G | U | U | A | U | A | U | G | G | c | U | G | A | U | G | U | c | a | U | -8 | 3 | 9 | c | false | <90% | 3265 | ||
| NM_001015048 | BAG5 | 1770 | 1788 | a | U | U | A | U | c | U | G | u | A | U | G | A | U | G | U | G | G | U | -25 | 3 | 10 | bc | false | <90% | 4840 | ||
| NM_004873 | BAG5 | 1777 | 1795 | a | U | U | A | U | c | U | G | u | A | U | G | A | U | G | U | G | G | U | -25 | 3 | 10 | bc | false | <90% | 4847 | ||
| NM_001015049 | BAG5 | 1936 | 1954 | a | U | U | A | U | c | U | G | u | A | U | G | A | U | G | U | G | G | U | -25 | 3 | 10 | bc | false | <90% | 5006 | ||
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_178499 | CCDC60 | 2025 | 2043 | A | a | C | A | C | A | U | C | A | U | C | C | A | U | A | U | g | c | C | 62 | 3 | 14 | ac | false | <90% | 2465 | ||
| NM_024814 | CBLL1 | 1454 | 1472 | A | C | C | A | C | A | U | C | A | U | C | C | A | g | A | U | c | A | g | 51 | 3 | 13 | c | false | <90% | 1978 | ||
| NM_001480 | GALR1 | 1558 | 1576 | A | C | C | A | C | A | U | C | A | U | C | C | A | U | c | U | c | u | g | 44 | 4 | 14 | c | false | <90% | 3056 | ||
| XM_938815 | LOC648154 | 82 | 100 | u | a | C | A | C | A | U | C | u | U | C | C | A | U | A | U | A | A | a | 21 | 4 | 9 | bc | false | <90% | 1638 | ||
| NM_014991 | WDFY3 | 4819 | 4837 | g | C | C | A | C | A | U | C | c | U | C | C | A | U | c | U | A | A | C | 13 | 3 | 7 | c | false | <90% | 14315 | ||
| NM_014554 | SENP1 | 1342 | 1360 | u | C | C | A | C | A | U | C | A | g | C | C | A | g | A | U | A | A | C | -4 | 3 | 8 | c | false | <90% | 4726 | ||
3 prime UTR Seed matches
Hits to same gene : 0
Hits to other genes : 2022
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