Automatic recommendation
Not OK - siRNA is not specific
17 hits were found for GCUAACAAAGAAGGCAUCG (9 guide strand hits and 8 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_144982 | CCDC131 | 3549 | 3567 | G | C | U | A | A | C | A | A | A | G | A | A | u | G | C | A | U | a | a | 81 | 3 | 12 | false | <90% | 7158 | |||
NM_145286 | STOML3 | 1858 | 1876 | c | a | a | A | A | C | A | A | A | G | A | A | G | G | C | A | U | a | G | 64 | 4 | 14 | c | false | <90% | 1954 | ||
NM_207315 | LOC129607 | 2040 | 2058 | a | C | U | u | A | C | A | A | A | G | A | A | G | G | C | A | U | u | G | 58 | 3 | 13 | c | false | <90% | 3009 | ||
NM_001033087 | C20orf133 | 3844 | 3862 | G | a | U | u | A | C | A | A | A | G | A | A | G | G | C | A | U | C | c | 46 | 3 | 14 | bc | false | <90% | 4425 | ||
NM_080676 | C20orf133 | 4282 | 4300 | G | a | U | u | A | C | A | A | A | G | A | A | G | G | C | A | U | C | c | 46 | 3 | 14 | bc | false | <90% | 4863 | ||
NM_025135 | FHOD3 | 3128 | 3146 | u | u | a | A | A | C | A | A | A | G | A | A | G | G | a | A | U | C | G | 42 | 4 | 11 | c | false | <90% | 4942 | ||
NM_182496 | CCDC38 | 1024 | 1042 | a | g | U | A | A | C | A | A | g | G | A | A | G | G | C | A | U | C | c | 21 | 4 | 9 | bc | false | <90% | 1953 | ||
NM_006731 | FCMD | 4477 | 4495 | c | u | U | A | A | C | A | g | A | G | A | A | G | G | C | A | U | C | c | 19 | 4 | 10 | bc | false | <90% | 7364 | ||
NM_001079802 | FCMD | 4569 | 4587 | c | u | U | A | A | C | A | g | A | G | A | A | G | G | C | A | U | C | c | 19 | 4 | 10 | bc | false | <90% | 7456 |
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_004827 | ABCG2 | 2002 | 2020 | a | G | A | U | G | C | C | U | U | C | U | U | c | G | U | U | A | u | g | 79 | 4 | 11 | false | <90% | 4445 | |||
NM_001004342 | TRIM67 | 7408 | 7426 | C | u | c | U | G | C | C | U | U | C | U | U | U | G | U | U | A | c | C | 66 | 3 | 14 | c | false | <90% | 8522 | ||
NM_014807 | TMEM24 | 3132 | 3150 | u | G | A | U | G | C | C | U | U | C | U | c | U | G | U | g | A | G | C | 38 | 3 | 10 | false | <90% | 3370 | |||
NM_152756 | RICTOR | 5551 | 5569 | a | G | A | U | G | C | C | U | U | g | U | U | U | G | U | U | A | a | C | 12 | 3 | 8 | c | false | <90% | 9535 | ||
NM_001408 | CELSR2 | 724 | 742 | g | G | A | U | G | C | C | c | U | C | U | U | U | G | a | U | A | G | C | 11 | 3 | 6 | c | false | <90% | 10531 | ||
NM_153647 | SLC24A4 | 325 | 343 | C | G | A | U | G | a | C | U | U | C | U | U | U | G | U | U | c | c | g | 5 | 4 | 10 | c | false | <90% | 4428 | ||
NM_153648 | SLC24A4 | 277 | 295 | C | G | A | U | G | a | C | U | U | C | U | U | U | G | U | U | c | c | g | 5 | 4 | 10 | c | false | <90% | 4437 | ||
NM_153646 | SLC24A4 | 325 | 343 | C | G | A | U | G | a | C | U | U | C | U | U | U | G | U | U | c | c | g | 5 | 4 | 10 | c | false | <90% | 4485 |
3 prime UTR Seed matches
Hits to same gene : 0
Hits to other genes : 1238
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