Automatic recommendation
OK - siRNA is specific for both sense and antisense (guide) strands
35 hits were found for CAGCAGAGUGCUGUGGAUG (19 guide strand hits and 16 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 | |||||||||||||
XM_001130080 | LOC643883 | 253 | 271 | g | g | G | C | A | G | A | G | U | G | C | U | G | U | G | G | g | c | G | 60 | 4 | 14 | ac | false | <90% | 720 | ||
XM_931880 | LOC643883 | 253 | 271 | g | g | G | C | A | G | A | G | U | G | C | U | G | U | G | G | g | c | G | 60 | 4 | 14 | ac | false | <90% | 720 | ||
NM_030812 | ACTL8 | 862 | 880 | C | A | G | C | A | G | A | G | U | G | C | c | u | U | G | G | A | U | G | 55 | 2 | 11 | false | <90% | 1852 | |||
NM_025224 | ZBTB46 | 970 | 988 | g | A | G | C | A | G | A | G | U | G | C | U | G | g | u | G | A | U | G | 53 | 3 | 12 | c | false | <90% | 4376 | ||
XM_927671 | ANKRD31 | 3952 | 3970 | C | A | G | a | A | G | A | G | U | G | C | U | u | U | G | G | A | U | G | 52 | 2 | 8 | false | <90% | 6036 | |||
XM_937397 | ANKRD31 | 3952 | 3970 | C | A | G | a | A | G | A | G | U | G | C | U | u | U | G | G | A | U | G | 52 | 2 | 8 | false | <90% | 6036 | |||
XM_001134399 | LOC730257 | 704 | 722 | C | A | a | C | A | G | A | G | U | G | C | U | G | U | u | G | A | U | u | 50 | 3 | 11 | c | false | <90% | 8141 | ||
XM_930678 | LOC642441 | 700 | 718 | C | A | a | C | A | G | A | G | U | G | C | U | G | U | u | G | A | U | u | 50 | 3 | 11 | c | false | <90% | 8151 | ||
XM_001134398 | LOC730256 | 704 | 722 | C | A | a | C | A | G | A | G | U | G | C | U | G | U | u | G | A | U | u | 50 | 3 | 11 | c | false | <90% | 8176 | ||
NM_007332 | TRPA1 | 4833 | 4851 | C | A | G | C | A | G | A | G | U | G | C | U | G | a | G | G | g | a | c | 49 | 4 | 13 | c | false | <90% | 5190 | ||
XR_017457 | LOC341674 | 504 | 522 | u | c | u | g | A | G | A | G | U | G | C | U | G | U | G | G | A | U | G | 30 | 4 | 15 | bc | false | <90% | 656 | ||
XR_019287 | LOC341674 | 504 | 522 | u | c | u | g | A | G | A | G | U | G | C | U | G | U | G | G | A | U | G | 30 | 4 | 15 | bc | false | <90% | 656 | ||
NM_012305 | AP2A2 | 1907 | 1925 | C | A | G | C | A | G | c | G | U | G | C | U | G | U | G | G | A | g | u | 26 | 3 | 10 | c | false | <90% | 4616 | ||
NM_005614 | RHEB | 870 | 888 | a | A | u | C | A | G | A | c | U | G | C | U | G | U | G | G | A | U | G | 16 | 3 | 11 | bc | false | <90% | 2092 | ||
NM_032293 | GARNL3 | 1802 | 1820 | C | A | G | C | A | G | A | G | a | G | C | U | G | a | G | G | A | U | u | 15 | 3 | 8 | c | false | <90% | 3362 | ||
NM_002146 | HOXB3 | 1304 | 1322 | C | A | G | C | A | G | A | G | g | G | C | U | G | U | G | G | u | g | G | 13 | 3 | 8 | c | false | <90% | 3627 | ||
NM_000623 | BDKRB2 | 2063 | 2081 | g | A | G | C | A | G | g | G | U | G | C | U | G | U | G | G | g | U | G | 8 | 3 | 9 | c | false | <90% | 4267 | ||
NM_020818 | KIAA1409 | 1290 | 1308 | C | A | G | C | A | G | g | G | U | G | C | U | G | U | G | G | u | c | G | 7 | 3 | 9 | c | false | <90% | 8471 | ||
NM_173562 | KCTD20 | 2472 | 2490 | C | A | G | C | A | c | A | u | U | G | C | U | G | U | G | G | A | U | a | -30 | 3 | 10 | bc | false | <90% | 5032 |
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_173527 | REM2 | 106 | 124 | a | A | a | C | C | A | C | A | G | C | A | C | U | C | U | G | C | c | c | 70 | 4 | 14 | c | false | <90% | 1885 | ||
NM_012295 | CABIN1 | 4982 | 5000 | g | g | a | C | C | A | C | A | G | C | A | C | c | C | U | G | C | U | G | 56 | 4 | 9 | false | <90% | 7222 | |||
NM_014030 | GIT1 | 1115 | 1133 | a | A | a | C | C | A | C | A | G | C | A | C | U | C | U | G | g | U | G | 54 | 3 | 13 | c | false | <90% | 3758 | ||
XR_019142 | LOC389948 | 698 | 716 | C | A | a | C | C | A | C | A | G | C | A | C | U | C | U | G | a | a | a | 49 | 4 | 13 | c | false | <90% | 739 | ||
XR_017185 | LOC389948 | 698 | 716 | C | A | a | C | C | A | C | A | G | C | A | C | U | C | U | G | a | a | a | 49 | 4 | 13 | c | false | <90% | 739 | ||
NM_194277 | FRMD7 | 129 | 147 | C | A | c | C | C | A | C | A | G | C | A | C | U | C | U | G | a | g | c | 49 | 4 | 13 | c | false | <90% | 3200 | ||
NM_024034 | GDAP1L1 | 1019 | 1037 | C | A | U | C | C | A | C | A | c | C | A | C | c | C | U | G | C | U | G | 29 | 2 | 8 | false | <90% | 2244 | |||
NM_173829 | P18SRP | 2206 | 2224 | u | A | U | C | C | A | C | A | G | C | c | C | U | C | U | G | C | a | u | 29 | 4 | 9 | c | false | <90% | 6856 | ||
NM_173039 | AQP11 | 887 | 905 | C | u | U | C | C | A | C | A | G | C | g | C | U | C | U | G | C | U | G | 27 | 2 | 8 | c | false | <90% | 1561 | ||
NM_015394 | ZNF10 | 136 | 154 | u | c | U | C | C | u | C | A | G | C | A | C | U | C | U | G | C | U | G | 23 | 3 | 13 | bc | false | <90% | 4417 | ||
NM_001017392 | SFRS14 | 4198 | 4216 | a | u | U | C | C | c | C | A | G | C | A | C | U | C | U | G | C | U | G | 23 | 3 | 13 | bc | false | <90% | 4715 | ||
XM_001125827 | LOC727820 | 7441 | 7459 | a | A | U | C | a | A | C | A | G | C | A | C | U | C | U | G | u | U | G | 23 | 3 | 11 | c | false | <90% | 8160 | ||
NM_031271 | TEX15 | 1019 | 1037 | C | A | U | C | C | u | C | A | G | C | A | C | U | C | U | G | u | g | G | 10 | 3 | 10 | c | false | <90% | 10155 | ||
NM_001058 | TACR1 | 146 | 164 | C | A | g | C | C | A | C | A | G | g | A | C | U | C | U | G | C | U | G | -2 | 2 | 9 | bc | false | <90% | 1766 | ||
NM_007236 | CHP | 1405 | 1423 | C | A | U | C | C | u | C | u | G | C | A | C | U | C | U | G | C | U | c | -30 | 3 | 10 | bc | false | <90% | 3248 | ||
NM_002673 | PLXNB1 | 5021 | 5039 | C | A | U | C | C | u | C | c | G | C | A | C | U | C | U | G | C | U | c | -30 | 3 | 10 | bc | false | <90% | 7097 |
3 prime UTR Seed matches
Hits to same gene : 0
Hits to other genes : 3170
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