Automatic recommendation
OK - siRNA is specific for both sense and antisense (guide) strands
25 hits were found for UGGUAUUGGGGGCCAAGUC (8 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_014598 | SOCS7 | 1321 | 1339 | U | G | G | U | A | U | U | G | G | G | G | G | C | C | A | A | u | g | a | 68 | 3 | 16 | ac | false | <90% | 2162 | ||
XM_936572 | SOCS7 | 1222 | 1240 | U | G | G | U | A | U | U | G | G | G | G | G | C | C | A | A | u | g | a | 68 | 3 | 16 | ac | false | <90% | 2206 | ||
XM_939163 | FLJ23152 | 96 | 114 | U | G | G | g | A | U | U | G | G | G | G | G | C | C | A | u | G | U | g | 32 | 3 | 11 | c | false | <90% | 2085 | ||
XM_376469 | FLJ23152 | 96 | 114 | U | G | G | g | A | U | U | G | G | G | G | G | C | C | A | u | G | U | g | 32 | 3 | 11 | c | false | <90% | 2085 | ||
NM_145062 | C6orf113 | 36 | 54 | a | G | G | U | A | c | U | G | G | G | G | G | C | C | A | A | G | g | u | 27 | 4 | 11 | c | false | <90% | 2197 | ||
NM_133336 | WHSC1 | 154 | 172 | U | G | u | U | u | U | U | G | G | G | G | G | C | C | A | A | G | U | a | 23 | 3 | 13 | bc | false | <90% | 3619 | ||
NM_003685 | KHSRP | 402 | 420 | U | G | G | U | u | U | U | G | G | G | G | G | C | C | A | A | a | a | g | 17 | 4 | 11 | c | false | <90% | 3009 | ||
NM_152557 | ZNF746 | 3348 | 3366 | U | G | G | g | u | U | U | G | G | G | G | G | C | C | A | A | G | U | g | 6 | 3 | 13 | bc | false | <90% | 3706 |
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_001248 | ENTPD3 | 1404 | 1422 | G | A | C | U | U | G | G | C | C | C | C | a | A | A | U | A | C | a | c | 58 | 3 | 11 | false | <90% | 2797 | |||
NM_020387 | RAB25 | 64 | 82 | G | A | g | U | U | G | G | C | C | C | C | C | A | A | U | c | C | C | u | 49 | 3 | 12 | c | false | <90% | 1101 | ||
NM_198462 | DCDC5 | 53 | 71 | a | A | C | U | U | G | G | C | C | C | C | C | A | A | U | u | a | C | A | 48 | 3 | 14 | c | false | <90% | 4483 | ||
NR_001447 | MT1L | 365 | 383 | G | u | u | U | U | G | G | C | C | C | C | C | A | A | U | c | C | C | A | 42 | 3 | 12 | c | false | <90% | 1117 | ||
NM_017564 | STAB2 | 4209 | 4227 | u | c | u | U | U | G | G | C | C | C | C | C | A | A | U | g | C | C | A | 40 | 4 | 12 | c | false | <90% | 8266 | ||
NM_016431 | MAPK8IP2 | 3031 | 3049 | u | c | C | U | g | G | G | C | C | C | C | C | A | A | U | A | C | C | c | 30 | 4 | 13 | bc | false | <90% | 3183 | ||
NM_012324 | MAPK8IP2 | 3229 | 3247 | u | c | C | U | g | G | G | C | C | C | C | C | A | A | U | A | C | C | c | 30 | 4 | 13 | bc | false | <90% | 3381 | ||
XM_498379 | LOC442461 | 528 | 546 | c | A | C | U | U | G | G | C | C | C | a | C | u | A | U | A | C | C | A | 26 | 3 | 9 | false | <90% | 669 | |||
XM_936655 | LOC442461 | 528 | 546 | c | A | C | U | U | G | G | C | C | C | a | C | u | A | U | A | C | C | A | 26 | 3 | 9 | false | <90% | 669 | |||
NM_001014433 | CUTA | 766 | 784 | G | A | C | U | g | G | G | C | C | C | C | C | A | A | U | A | a | a | u | 17 | 4 | 11 | c | false | <90% | 823 | ||
NM_001014840 | CUTA | 894 | 912 | G | A | C | U | g | G | G | C | C | C | C | C | A | A | U | A | a | a | u | 17 | 4 | 11 | c | false | <90% | 951 | ||
NM_001014838 | CUTA | 984 | 1002 | G | A | C | U | g | G | G | C | C | C | C | C | A | A | U | A | a | a | u | 17 | 4 | 11 | c | false | <90% | 1041 | ||
NM_001014837 | CUTA | 1015 | 1033 | G | A | C | U | g | G | G | C | C | C | C | C | A | A | U | A | a | a | u | 17 | 4 | 11 | c | false | <90% | 1072 | ||
NM_015921 | CUTA | 1157 | 1175 | G | A | C | U | g | G | G | C | C | C | C | C | A | A | U | A | a | a | u | 17 | 4 | 11 | c | false | <90% | 1214 | ||
NM_002206 | ITGA7 | 927 | 945 | G | A | C | U | U | G | G | C | C | C | u | C | A | A | U | A | g | C | u | 10 | 3 | 10 | c | false | <90% | 4079 | ||
NM_014784 | ARHGEF11 | 2457 | 2475 | G | A | C | U | U | c | G | C | C | C | u | C | A | A | U | A | C | C | u | -29 | 3 | 7 | c | false | <90% | 6784 | ||
NM_198236 | ARHGEF11 | 2577 | 2595 | G | A | C | U | U | c | G | C | C | C | u | C | A | A | U | A | C | C | u | -29 | 3 | 7 | c | false | <90% | 6904 |
3 prime UTR Seed matches
Hits to same gene : 0
Hits to other genes : 2488
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