Automatic recommendation
OK - siRNA is specific for both sense and antisense (guide) strands
11 hits were found for GCGUGUUAAAAAUCUGAAC (4 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_001079872 | CUL4B | 4409 | 4427 | G | u | u | U | G | U | U | A | A | A | A | A | U | C | a | G | A | A | C | 44 | 3 | 11 | c | false | <90% | 5198 | ||
NM_003588 | CUL4B | 4576 | 4594 | G | u | u | U | G | U | U | A | A | A | A | A | U | C | a | G | A | A | C | 44 | 3 | 11 | c | false | <90% | 5365 | ||
NM_025114 | CEP290 | 5448 | 5466 | c | a | G | U | G | U | U | u | A | A | A | A | U | C | U | G | A | A | C | 24 | 3 | 11 | bc | false | <90% | 7972 | ||
NM_033426 | KIAA1737 | 3503 | 3521 | c | u | G | U | G | U | c | A | A | A | A | A | U | C | U | G | A | A | a | 15 | 4 | 11 | bc | false | <90% | 4397 |
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_004859 | CLTC | 704 | 722 | c | U | U | C | A | G | A | U | U | U | U | U | A | A | C | A | u | u | g | 66 | 4 | 15 | ac | false | <90% | 8575 | ||
NM_002576 | PAK1 | 593 | 611 | c | U | U | C | A | G | A | U | U | U | U | g | A | A | C | A | C | a | C | 61 | 3 | 10 | false | <90% | 3264 | |||
XM_001129251 | HEG1 | 8640 | 8658 | a | U | U | C | A | G | A | U | U | U | U | U | A | A | a | A | u | G | C | 49 | 3 | 13 | c | false | <90% | 9136 | ||
XM_087386 | HEG1 | 8717 | 8735 | a | U | U | C | A | G | A | U | U | U | U | U | A | A | a | A | u | G | C | 49 | 3 | 13 | c | false | <90% | 9213 | ||
NM_025151 | RAB11FIP1 | 2597 | 2615 | u | U | U | C | A | G | A | U | U | U | U | g | A | A | C | A | a | G | C | 40 | 3 | 10 | false | <90% | 4222 | |||
NM_001002233 | RAB11FIP1 | 2932 | 2950 | u | U | U | C | A | G | A | U | U | U | U | g | A | A | C | A | a | G | C | 40 | 3 | 10 | false | <90% | 4557 | |||
NM_001002814 | RAB11FIP1 | 4499 | 4517 | u | U | U | C | A | G | A | U | U | U | U | g | A | A | C | A | a | G | C | 40 | 3 | 10 | false | <90% | 7839 |
3 prime UTR Seed matches
Hits to same gene : 0
Hits to other genes : 477
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