Automatic recommendation
OK - siRNA is specific for both sense and antisense (guide) strands
11 hits were found for CAUUGUUCACCUCACCAUA (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_015465 | GEMIN5 | 472 | 490 | a | c | U | U | G | U | U | C | A | C | C | U | C | A | u | C | A | U | g | 56 | 4 | 12 | c | false | <90% | 4527 | ||
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_198445 | FLJ45909 | 108 | 126 | g | g | g | G | G | U | G | A | G | G | U | G | A | A | C | A | A | a | G | 64 | 4 | 14 | c | false | <90% | 3021 | ||
| NM_006514 | SCN10A | 2710 | 2728 | g | A | U | G | G | g | G | A | G | G | U | G | A | A | C | A | A | c | c | 27 | 4 | 11 | c | false | <90% | 5874 | ||
| NM_001033853 | RPL3 | 889 | 907 | U | A | U | G | G | U | G | A | a | G | U | G | A | c | C | A | A | U | G | 20 | 2 | 8 | c | false | <90% | 1201 | ||
| XR_018187 | LOC647722 | 967 | 985 | U | A | U | G | G | U | G | A | a | G | U | G | A | c | C | A | A | U | G | 20 | 2 | 8 | c | false | <90% | 1213 | ||
| XR_017039 | LOC645798 | 967 | 985 | U | A | U | G | G | U | G | A | a | G | U | G | A | c | C | A | A | U | G | 20 | 2 | 8 | c | false | <90% | 1213 | ||
| XR_016530 | LOC643220 | 960 | 978 | U | A | U | G | G | U | G | A | a | G | U | G | A | c | C | A | A | U | G | 20 | 2 | 8 | c | false | <90% | 1256 | ||
| XR_019077 | LOC642741 | 994 | 1012 | U | A | U | G | G | U | G | A | a | G | U | G | A | c | C | A | A | U | G | 20 | 2 | 8 | c | false | <90% | 1310 | ||
| XR_016455 | LOC642741 | 994 | 1012 | U | A | U | G | G | U | G | A | a | G | U | G | A | c | C | A | A | U | G | 20 | 2 | 8 | c | false | <90% | 1310 | ||
| NM_000967 | RPL3 | 1036 | 1054 | U | A | U | G | G | U | G | A | a | G | U | G | A | c | C | A | A | U | G | 20 | 2 | 8 | c | false | <90% | 1348 | ||
| NM_052947 | ALPK2 | 126 | 144 | g | A | U | G | G | U | G | A | c | c | U | G | A | A | C | A | A | U | G | -44 | 3 | 9 | bc | false | <90% | 6496 | ||
3 prime UTR Seed matches
Hits to same gene : 0
Hits to other genes : 3107
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