Automatic recommendation
OK - siRNA is specific for both sense and antisense (guide) strands
20 hits were found for GCCAUCUGUGUGCUUAAGA (13 guide strand hits and 7 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_001723 | DST | 1926 | 1944 | c | C | C | A | U | C | U | G | U | G | U | G | C | U | U | c | A | c | c | 64 | 4 | 14 | c | false | <90% | 8972 | ||
NM_020388 | DST | 1926 | 1944 | c | C | C | A | U | C | U | G | U | G | U | G | C | U | U | c | A | c | c | 64 | 4 | 14 | c | false | <90% | 9348 | ||
NM_015548 | DST | 1926 | 1944 | c | C | C | A | U | C | U | G | U | G | U | G | C | U | U | c | A | c | c | 64 | 4 | 14 | c | false | <90% | 16384 | ||
NM_183380 | DST | 3322 | 3340 | c | C | C | A | U | C | U | G | U | G | U | G | C | U | U | c | A | c | c | 64 | 4 | 14 | c | false | <90% | 18036 | ||
NM_000232 | SGCB | 214 | 232 | G | C | C | A | U | C | U | G | U | G | U | G | a | U | U | A | u | c | c | 58 | 4 | 12 | false | <90% | 4229 | |||
XR_016198 | LOC642697 | 801 | 819 | G | C | C | A | U | C | U | G | U | G | U | c | C | U | U | A | g | G | A | 42 | 2 | 11 | false | <90% | 867 | |||
NM_017735 | TTC27 | 1241 | 1259 | c | g | g | A | U | C | U | G | U | G | U | G | C | U | g | A | A | G | A | 42 | 4 | 11 | c | false | <90% | 2945 | ||
NM_031455 | CCDC3 | 2119 | 2137 | c | C | C | A | g | C | U | G | U | G | U | G | a | U | U | A | A | G | A | 36 | 3 | 7 | false | <90% | 2753 | |||
NM_012426 | SF3B3 | 1213 | 1231 | G | C | C | A | U | g | U | G | U | G | U | G | C | U | U | A | A | a | A | 34 | 2 | 11 | c | false | <90% | 4357 | ||
NM_000194 | HPRT1 | 275 | 293 | G | C | C | c | U | C | U | G | U | G | U | G | C | U | c | A | A | G | g | 33 | 3 | 10 | c | false | <90% | 1331 | ||
NM_015296 | DOCK9 | 3461 | 3479 | G | C | C | A | U | C | a | G | U | G | U | G | C | U | c | A | A | G | A | 9 | 2 | 7 | c | false | <90% | 7522 | ||
XR_017737 | C21orf77 | 928 | 946 | G | C | C | A | U | C | U | G | U | c | U | G | C | U | U | c | A | G | A | -8 | 2 | 9 | c | false | <90% | 1452 | ||
XR_017792 | C21orf77 | 928 | 946 | G | C | C | A | U | C | U | G | U | c | U | G | C | U | U | c | A | G | A | -8 | 2 | 9 | c | false | <90% | 1452 |
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_012256 | ZNF212 | 2622 | 2640 | g | a | a | a | A | A | G | C | A | C | A | C | A | G | A | U | G | G | C | 30 | 4 | 15 | bc | false | <90% | 2796 | ||
XM_039570 | SEC15L2 | 5184 | 5202 | g | g | g | c | A | A | G | C | A | C | A | C | A | G | A | U | G | G | C | 30 | 4 | 15 | bc | false | <90% | 6018 | ||
XM_945916 | SEC15L2 | 5184 | 5202 | g | g | g | c | A | A | G | C | A | C | A | C | A | G | A | U | G | G | C | 30 | 4 | 15 | bc | false | <90% | 6018 | ||
NM_138775 | ALKBH8 | 820 | 838 | U | u | U | U | A | A | G | C | A | C | c | C | A | G | A | U | G | G | C | 27 | 2 | 8 | c | false | <90% | 1685 | ||
NM_000216 | KAL1 | 2120 | 2138 | U | C | U | U | c | A | G | C | A | C | A | C | A | G | A | U | c | u | C | 22 | 3 | 11 | c | false | <90% | 6314 | ||
NM_173807 | C1orf101 | 486 | 504 | U | a | c | U | c | A | G | C | A | C | A | C | A | G | A | U | G | G | C | 17 | 3 | 14 | bc | false | <90% | 3036 | ||
NM_004685 | MTMR6 | 1946 | 1964 | a | a | a | U | A | A | G | C | A | a | A | C | A | G | A | U | G | G | C | -15 | 4 | 9 | bc | false | <90% | 5222 |
3 prime UTR Seed matches
Hits to same gene : 0
Hits to other genes : 2093
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)
Motif found in guide strand
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