Automatic recommendation
OK - siRNA is specific for both sense and antisense (guide) strands
15 hits were found for GGAAUGAGGAGCUACAUAG (9 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 | |||||||||||||
XR_015474 | LOC728640 | 220 | 238 | G | G | A | A | U | G | A | G | G | A | G | u | U | A | C | A | U | u | c | 58 | 3 | 11 | false | <90% | 2520 | |||
XR_015400 | LOC730753 | 220 | 238 | G | G | A | A | U | G | A | G | G | A | G | u | U | A | C | A | U | u | c | 58 | 3 | 11 | false | <90% | 2521 | |||
NM_001133 | AFM | 1647 | 1665 | a | G | A | A | U | G | A | G | G | A | G | C | U | u | C | A | g | A | G | 54 | 3 | 12 | c | false | <90% | 1997 | ||
NM_015229 | KIAA0664 | 1156 | 1174 | G | G | A | A | U | G | A | G | G | A | G | C | U | g | C | A | g | A | c | 51 | 3 | 13 | c | false | <90% | 5252 | ||
NM_015065 | EXPH5 | 177 | 195 | G | G | A | A | U | G | A | G | G | A | G | u | U | A | C | A | g | A | G | 42 | 2 | 11 | false | <90% | 6655 | |||
NM_145755 | TTC21A | 2043 | 2061 | u | G | A | A | U | G | g | G | G | A | G | C | U | A | C | A | U | g | a | 24 | 4 | 10 | c | false | <90% | 4233 | ||
NM_001005502 | CPM | 4249 | 4267 | G | G | A | A | U | G | A | a | G | A | G | C | U | A | C | A | g | g | a | 6 | 4 | 8 | c | false | <90% | 6651 | ||
NM_198320 | CPM | 4267 | 4285 | G | G | A | A | U | G | A | a | G | A | G | C | U | A | C | A | g | g | a | 6 | 4 | 8 | c | false | <90% | 6669 | ||
NM_001874 | CPM | 4281 | 4299 | G | G | A | A | U | G | A | a | G | A | G | C | U | A | C | A | g | g | a | 6 | 4 | 8 | c | false | <90% | 6683 |
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 | |||||||||||||
XM_001127587 | FLJ32810 | 2753 | 2771 | C | U | A | U | G | U | A | G | C | U | C | C | U | u | A | U | U | a | a | 72 | 3 | 13 | c | false | <90% | 4820 | ||
XM_001127623 | FLJ32810 | 2753 | 2771 | C | U | A | U | G | U | A | G | C | U | C | C | U | u | A | U | U | a | a | 72 | 3 | 13 | c | false | <90% | 4820 | ||
XM_925815 | FLJ32810 | 2753 | 2771 | C | U | A | U | G | U | A | G | C | U | C | C | U | u | A | U | U | a | a | 72 | 3 | 13 | c | false | <90% | 4820 | ||
XM_001127637 | FLJ32810 | 2756 | 2774 | C | U | A | U | G | U | A | G | C | U | C | C | U | u | A | U | U | a | a | 72 | 3 | 13 | c | false | <90% | 4823 | ||
XM_001127597 | FLJ32810 | 2762 | 2780 | C | U | A | U | G | U | A | G | C | U | C | C | U | u | A | U | U | a | a | 72 | 3 | 13 | c | false | <90% | 4829 | ||
NM_005621 | S100A12 | 21 | 39 | u | g | c | U | G | U | A | G | C | U | C | C | a | C | A | U | U | C | C | 56 | 4 | 9 | false | <90% | 466 |
3 prime UTR Seed matches
Hits to same gene : 0
Hits to other genes : 2270
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