Automatic recommendation
OK - siRNA is specific for both sense and antisense (guide) strands
21 hits were found for GGUAUGUUAACUAAUAAAU (8 guide strand hits and 13 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 | |||||||||||||
NR_003366 | ANKRD20B | 18663 | 18681 | a | u | U | A | U | G | U | U | A | A | C | U | A | A | g | A | A | A | a | 56 | 4 | 12 | c | false | <90% | 96524 | ||
NM_005721 | ACTR3 | 2407 | 2425 | u | a | U | A | a | G | U | U | A | A | C | U | A | A | U | A | A | A | U | 35 | 3 | 14 | bc | false | <90% | 2728 | ||
NM_007249 | KLF12 | 4060 | 4078 | G | G | U | A | a | G | U | U | A | A | C | U | g | A | U | A | A | A | a | 33 | 3 | 7 | false | <90% | 10923 | |||
NM_144964 | RG9MTD3 | 1529 | 1547 | G | a | U | A | U | G | U | U | A | A | g | U | A | A | U | A | A | A | a | 22 | 3 | 8 | c | false | <90% | 2293 | ||
NM_012223 | MYO1B | 4633 | 4651 | a | u | U | A | U | G | U | U | A | A | a | U | A | A | U | A | A | A | a | 20 | 4 | 8 | c | false | <90% | 4825 | ||
NM_212460 | ARL4A | 1708 | 1726 | G | G | c | A | U | G | U | a | A | A | C | U | A | A | U | A | A | A | U | 18 | 2 | 11 | bc | false | <90% | 2954 | ||
NM_001037164 | ARL4A | 1711 | 1729 | G | G | c | A | U | G | U | a | A | A | C | U | A | A | U | A | A | A | U | 18 | 2 | 11 | bc | false | <90% | 2957 | ||
NM_005738 | ARL4A | 1916 | 1934 | G | G | c | A | U | G | U | a | A | A | C | U | A | A | U | A | A | A | U | 18 | 2 | 11 | bc | false | <90% | 3162 |
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_007347 | AP4E1 | 3045 | 3063 | u | U | U | U | A | U | U | A | G | U | U | A | u | C | A | U | A | u | g | 79 | 4 | 11 | false | <90% | 6682 | |||
NM_001018076 | NR3C1 | 2678 | 2696 | A | U | U | U | A | U | U | A | G | U | U | A | A | u | A | U | A | u | C | 77 | 2 | 13 | c | false | <90% | 6410 | ||
NM_001018075 | NR3C1 | 2785 | 2803 | A | U | U | U | A | U | U | A | G | U | U | A | A | u | A | U | A | u | C | 77 | 2 | 13 | c | false | <90% | 6517 | ||
NM_001018074 | NR3C1 | 2882 | 2900 | A | U | U | U | A | U | U | A | G | U | U | A | A | u | A | U | A | u | C | 77 | 2 | 13 | c | false | <90% | 6614 | ||
NM_000176 | NR3C1 | 3052 | 3070 | A | U | U | U | A | U | U | A | G | U | U | A | A | u | A | U | A | u | C | 77 | 2 | 13 | c | false | <90% | 6784 | ||
NM_001024094 | NR3C1 | 3055 | 3073 | A | U | U | U | A | U | U | A | G | U | U | A | A | u | A | U | A | u | C | 77 | 2 | 13 | c | false | <90% | 6787 | ||
NM_001018077 | NR3C1 | 3554 | 3572 | A | U | U | U | A | U | U | A | G | U | U | A | A | u | A | U | A | u | C | 77 | 2 | 13 | c | false | <90% | 7286 | ||
NM_018724 | IL20 | 812 | 830 | A | U | U | U | A | U | U | A | G | U | U | A | A | u | A | U | A | u | u | 72 | 3 | 13 | c | false | <90% | 1252 | ||
NM_213651 | SLC25A24 | 1113 | 1131 | A | U | U | U | A | U | U | A | G | g | U | A | u | C | A | U | A | C | C | 6 | 2 | 9 | false | <90% | 3344 | |||
NM_013386 | SLC25A24 | 1188 | 1206 | A | U | U | U | A | U | U | A | G | g | U | A | u | C | A | U | A | C | C | 6 | 2 | 9 | false | <90% | 3423 | |||
NM_144578 | C14orf32 | 2334 | 2352 | A | U | U | U | A | U | U | A | G | a | U | A | A | C | A | U | u | u | u | -13 | 4 | 9 | c | false | <90% | 6469 | ||
XM_940636 | ZNF594 | 3711 | 3729 | A | U | U | U | A | U | U | u | u | U | U | A | A | C | A | U | A | C | a | -27 | 3 | 9 | bc | false | <90% | 4863 | ||
XM_290737 | ZNF594 | 3711 | 3729 | A | U | U | U | A | U | U | u | u | U | U | A | A | C | A | U | A | C | a | -27 | 3 | 9 | bc | false | <90% | 4863 |
3 prime UTR Seed matches
Hits to same gene : 0
Hits to other genes : 1235
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