Automatic recommendation
OK - siRNA is specific for both sense and antisense (guide) strands
12 hits were found for GUUCCGUGCUAUUGAGAAA (6 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_033048 | CPXCR1 | 913 | 931 | a | U | U | C | C | G | U | G | C | U | A | U | U | G | u | G | A | g | g | 65 | 4 | 13 | c | false | <90% | 1609 | ||
NM_016413 | CPB2 | 976 | 994 | a | g | U | u | C | G | U | G | C | U | A | U | U | G | A | G | A | A | A | 49 | 3 | 15 | bc | false | <90% | 1603 | ||
NM_001872 | CPB2 | 1087 | 1105 | a | g | U | u | C | G | U | G | C | U | A | U | U | G | A | G | A | A | A | 49 | 3 | 15 | bc | false | <90% | 1766 | ||
NM_004999 | MYO6 | 5593 | 5611 | u | g | U | C | u | G | U | G | C | U | A | U | U | G | A | G | A | A | u | 30 | 4 | 13 | bc | false | <90% | 8662 | ||
XM_938514 | PRPF40A | 3761 | 3779 | u | U | U | C | C | c | U | G | C | U | A | U | U | G | A | G | g | A | A | 11 | 3 | 10 | c | false | <90% | 7651 | ||
XM_371575 | PRPF40A | 4390 | 4408 | u | U | U | C | C | c | U | G | C | U | A | U | U | G | A | G | g | A | A | 11 | 3 | 10 | c | false | <90% | 8280 |
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_003112 | SP4 | 2943 | 2961 | U | U | U | C | U | C | u | A | U | A | G | C | A | C | a | G | A | A | a | 4 | 3 | 7 | c | false | <90% | 5811 | ||
NM_153277 | SLC22A6 | 575 | 593 | U | U | U | C | U | C | A | A | U | g | G | C | A | C | a | G | A | A | g | -12 | 3 | 9 | c | false | <90% | 2025 | ||
NM_153278 | SLC22A6 | 575 | 593 | U | U | U | C | U | C | A | A | U | g | G | C | A | C | a | G | A | A | g | -12 | 3 | 9 | c | false | <90% | 2064 | ||
NM_153279 | SLC22A6 | 512 | 530 | U | U | U | C | U | C | A | A | U | g | G | C | A | C | a | G | A | A | g | -12 | 3 | 9 | c | false | <90% | 2131 | ||
NM_153276 | SLC22A6 | 575 | 593 | U | U | U | C | U | C | A | A | U | g | G | C | A | C | a | G | A | A | g | -12 | 3 | 9 | c | false | <90% | 2194 | ||
NM_004790 | SLC22A6 | 575 | 593 | U | U | U | C | U | C | A | A | U | g | G | C | A | C | a | G | A | A | g | -12 | 3 | 9 | c | false | <90% | 2196 |
3 prime UTR Seed matches
Hits to same gene : 0
Hits to other genes : 356
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