Automatic recommendation
OK - siRNA is specific for both sense and antisense (guide) strands
20 hits were found for GGCUGCUUAUGGUGACAAU (6 guide strand hits and 14 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_024952 | C14orf159 | 2518 | 2536 | a | G | C | U | G | C | U | U | c | U | G | G | c | G | A | C | A | A | U | 27 | 3 | 7 | false | <90% | 2985 | |||
NM_019592 | RNF20 | 2973 | 2991 | u | G | C | U | G | C | U | U | u | U | G | G | U | G | c | C | A | A | U | 13 | 3 | 7 | c | false | <90% | 3970 | ||
NM_000766 | CYP2A13 | 23 | 41 | G | G | C | U | G | C | U | U | c | U | G | G | U | G | A | C | c | u | U | 13 | 3 | 8 | c | false | <90% | 1747 | ||
NM_032445 | MEGF11 | 5332 | 5350 | G | u | g | U | G | a | U | U | A | U | G | G | U | G | A | C | A | A | U | 5 | 3 | 13 | bc | false | <90% | 5702 | ||
NM_002576 | PAK1 | 342 | 360 | u | G | C | U | G | C | U | g | g | U | G | G | U | G | A | C | A | A | U | -24 | 3 | 10 | bc | false | <90% | 3264 | ||
NM_014809 | KIAA0319 | 557 | 575 | u | G | C | U | G | C | U | g | c | U | G | G | U | G | A | C | A | A | U | -24 | 3 | 10 | bc | false | <90% | 6805 |
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_152491 | FLJ32569 | 2110 | 2128 | A | U | U | G | U | C | A | C | C | A | U | A | A | u | C | A | G | u | C | 77 | 2 | 13 | c | false | <90% | 2265 | ||
XR_018417 | LOC401847 | 432 | 450 | u | U | U | G | U | C | A | C | C | A | U | g | A | c | C | A | G | C | C | 44 | 3 | 10 | false | <90% | 516 | |||
XR_017500 | LOC401847 | 432 | 450 | u | U | U | G | U | C | A | C | C | A | U | g | A | c | C | A | G | C | C | 44 | 3 | 10 | false | <90% | 516 | |||
NM_178543 | ENPP7 | 233 | 251 | u | U | U | G | U | C | A | C | C | A | U | g | A | c | C | A | G | C | C | 44 | 3 | 10 | false | <90% | 1877 | |||
NM_005647 | TBL1X | 595 | 613 | g | a | a | G | U | C | A | C | C | A | U | A | A | G | g | A | G | C | C | 42 | 4 | 11 | c | false | <90% | 5886 | ||
NM_020666 | CLK4 | 1334 | 1352 | A | U | U | u | U | C | A | C | C | A | U | A | A | c | C | A | G | C | u | 38 | 3 | 9 | c | false | <90% | 2524 | ||
NM_025112 | ZXDC | 440 | 458 | g | c | c | G | U | C | A | C | C | A | U | c | A | G | C | A | G | C | C | 33 | 4 | 8 | false | <90% | 3410 | |||
NM_001040653 | ZXDC | 440 | 458 | g | c | c | G | U | C | A | C | C | A | U | c | A | G | C | A | G | C | C | 33 | 4 | 8 | false | <90% | 4888 | |||
NM_001081752 | ELN | 1164 | 1182 | u | g | U | G | U | C | A | C | C | A | g | A | A | G | C | A | G | C | u | 20 | 4 | 8 | c | false | <90% | 3339 | ||
NM_001081753 | ELN | 1209 | 1227 | u | g | U | G | U | C | A | C | C | A | g | A | A | G | C | A | G | C | u | 20 | 4 | 8 | c | false | <90% | 3384 | ||
NM_001081755 | ELN | 1194 | 1212 | u | g | U | G | U | C | A | C | C | A | g | A | A | G | C | A | G | C | u | 20 | 4 | 8 | c | false | <90% | 3423 | ||
NM_001081754 | ELN | 1209 | 1227 | u | g | U | G | U | C | A | C | C | A | g | A | A | G | C | A | G | C | u | 20 | 4 | 8 | c | false | <90% | 3441 | ||
NM_000501 | ELN | 1194 | 1212 | u | g | U | G | U | C | A | C | C | A | g | A | A | G | C | A | G | C | u | 20 | 4 | 8 | c | false | <90% | 3480 | ||
NM_015510 | DHRS7B | 592 | 610 | A | U | U | G | U | C | g | C | C | A | U | c | A | G | C | A | G | C | a | -5 | 3 | 6 | false | <90% | 1377 |
3 prime UTR Seed matches
Hits to same gene : 0
Hits to other genes : 3054
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