Automatic recommendation
OK - siRNA is specific for both sense and antisense (guide) strands
24 hits were found for CAUGGAGAACAUCACAUCA (7 guide strand hits and 17 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_018256 | WDR12 | 408 | 426 | a | g | U | G | G | A | G | A | A | C | A | U | C | u | C | A | U | C | A | 67 | 3 | 11 | c | false | <90% | 1720 | ||
NM_152265 | BTF3L4 | 639 | 657 | C | A | U | G | G | A | G | A | A | C | A | U | C | A | C | c | U | g | u | 66 | 3 | 15 | c | false | <90% | 2201 | ||
NM_001032998 | KYNU | 1154 | 1172 | u | A | U | G | G | A | G | A | A | C | A | U | C | A | a | A | U | a | c | 65 | 4 | 13 | c | false | <90% | 1315 | ||
NM_005893 | CCIN | 835 | 853 | C | A | U | G | G | A | G | A | A | C | A | c | C | u | C | A | U | C | c | 41 | 3 | 11 | false | <90% | 1930 | |||
XM_371949 | LOC442721 | 660 | 678 | C | A | U | u | G | A | G | A | A | C | A | U | C | A | C | A | a | C | A | 39 | 2 | 12 | c | false | <90% | 1626 | ||
XM_937717 | LOC442721 | 660 | 678 | C | A | U | u | G | A | G | A | A | C | A | U | C | A | C | A | a | C | A | 39 | 2 | 12 | c | false | <90% | 1626 | ||
XM_499467 | LOC442721 | 660 | 678 | C | A | U | u | G | A | G | A | A | C | A | U | C | A | C | A | a | C | A | 39 | 2 | 12 | c | false | <90% | 1626 |
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_004901 | ENTPD4 | 1090 | 1108 | g | G | A | U | G | U | G | A | U | G | U | U | C | a | C | C | A | a | a | 70 | 4 | 12 | c | false | <90% | 2329 | ||
NR_002177 | TTTY4C | 631 | 649 | U | a | A | U | G | U | G | A | U | G | U | U | C | c | C | C | A | U | u | 64 | 3 | 11 | c | false | <90% | 1346 | ||
NR_002178 | TTTY4B | 631 | 649 | U | a | A | U | G | U | G | A | U | G | U | U | C | c | C | C | A | U | u | 64 | 3 | 11 | c | false | <90% | 1346 | ||
NR_001525 | TTTY4 | 631 | 649 | U | a | A | U | G | U | G | A | U | G | U | U | C | c | C | C | A | U | u | 64 | 3 | 11 | c | false | <90% | 1370 | ||
NM_001037162 | ACOT6 | 133 | 151 | a | u | u | U | G | U | G | A | U | G | U | U | C | U | C | C | A | g | G | 64 | 4 | 14 | c | false | <90% | 1004 | ||
NM_000452 | SLC10A2 | 732 | 750 | c | u | u | g | G | U | G | A | U | G | U | U | C | U | C | C | A | U | G | 30 | 4 | 15 | bc | false | <90% | 3779 | ||
NM_144565 | DUOXA1 | 985 | 1003 | c | a | A | U | G | U | G | A | U | G | c | U | C | U | C | C | A | U | G | 25 | 3 | 8 | c | false | <90% | 1923 | ||
XR_018084 | LOC389652 | 1661 | 1679 | U | u | g | U | u | U | G | A | U | G | U | U | C | U | C | C | A | U | G | 17 | 3 | 14 | bc | false | <90% | 2145 | ||
NM_002717 | PPP2R2A | 1823 | 1841 | c | a | c | U | G | U | G | g | U | G | U | U | C | U | C | C | A | U | G | 4 | 4 | 11 | bc | false | <90% | 2385 | ||
NM_001430 | EPAS1 | 1539 | 1557 | U | G | A | c | G | U | G | g | U | G | U | U | C | U | C | C | A | U | G | 1 | 2 | 11 | bc | false | <90% | 5186 | ||
NM_198578 | LRRK2 | 1319 | 1337 | g | G | A | a | G | U | G | A | U | G | c | U | C | U | C | C | A | U | G | 0 | 3 | 8 | c | false | <90% | 9234 | ||
NM_006422 | AKAP3 | 1111 | 1129 | U | G | A | U | a | U | G | A | U | G | g | U | C | U | C | C | A | U | c | -17 | 3 | 7 | c | false | <90% | 3027 | ||
NM_177963 | SYT12 | 715 | 733 | U | G | A | U | G | a | G | A | a | G | U | U | C | U | C | C | A | U | c | -28 | 3 | 9 | bc | false | <90% | 3520 | ||
NM_173054 | RELN | 10572 | 10590 | U | G | A | U | G | U | G | u | U | G | c | U | C | U | C | C | A | U | u | -28 | 3 | 7 | c | false | <90% | 11558 | ||
NM_005045 | RELN | 10578 | 10596 | U | G | A | U | G | U | G | u | U | G | c | U | C | U | C | C | A | U | u | -28 | 3 | 7 | c | false | <90% | 11564 | ||
NM_052820 | CORO2A | 624 | 642 | a | G | A | U | G | U | G | A | U | c | c | U | C | U | C | C | A | U | G | -46 | 3 | 8 | c | false | <90% | 2265 | ||
NM_003389 | CORO2A | 808 | 826 | a | G | A | U | G | U | G | A | U | c | c | U | C | U | C | C | A | U | G | -46 | 3 | 8 | c | false | <90% | 2427 |
3 prime UTR Seed matches
Hits to same gene : 0
Hits to other genes : 2457
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