Automatic recommendation
OK - siRNA is specific for both sense and antisense (guide) strands
35 hits were found for GGAUGAGGAAGGCAAUUUA (26 guide strand hits and 9 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_001005332 | MAGED1 | 2246 | 2264 | G | G | A | U | G | A | G | G | A | A | G | G | a | g | A | U | U | U | u | 65 | 3 | 12 | false | <90% | 2665 | |||
NM_006986 | MAGED1 | 2341 | 2359 | G | G | A | U | G | A | G | G | A | A | G | G | a | g | A | U | U | U | u | 65 | 3 | 12 | false | <90% | 2760 | |||
NM_001005333 | MAGED1 | 2509 | 2527 | G | G | A | U | G | A | G | G | A | A | G | G | a | g | A | U | U | U | u | 65 | 3 | 12 | false | <90% | 2928 | |||
XM_940667 | SDC3 | 2764 | 2782 | G | G | c | U | G | A | G | G | A | A | G | G | a | A | A | U | U | U | g | 65 | 3 | 9 | false | <90% | 5147 | |||
NM_002198 | IRF1 | 878 | 896 | G | G | A | U | G | A | G | G | A | A | G | G | g | A | A | a | U | U | A | 63 | 2 | 12 | false | <90% | 2035 | |||
NM_022089 | ATP13A2 | 663 | 681 | u | G | g | U | G | A | G | G | A | A | G | G | C | c | A | U | U | U | A | 58 | 3 | 10 | c | false | <90% | 3840 | ||
NM_001015509 | PTRH2 | 463 | 481 | a | G | A | a | G | A | G | G | A | A | G | G | C | A | A | U | U | a | c | 53 | 4 | 13 | c | false | <90% | 2123 | ||
NM_181503 | EXOSC8 | 704 | 722 | G | G | A | U | G | A | G | G | A | A | G | G | C | A | A | a | c | U | c | 45 | 3 | 15 | c | false | <90% | 986 | ||
NM_016269 | LEF1 | 786 | 804 | c | G | A | a | G | A | G | G | A | A | G | G | C | g | A | U | U | U | A | 41 | 3 | 9 | c | false | <90% | 3084 | ||
NM_032095 | PCDHGB1 | 471 | 489 | a | G | A | U | G | u | G | G | A | A | G | G | C | A | A | U | U | c | A | 32 | 3 | 11 | c | false | <90% | 2433 | ||
NM_018922 | PCDHGB1 | 471 | 489 | a | G | A | U | G | u | G | G | A | A | G | G | C | A | A | U | U | c | A | 32 | 3 | 11 | c | false | <90% | 4590 | ||
NM_001007795 | TTC6 | 393 | 411 | c | a | u | g | G | A | G | G | A | A | G | G | C | A | A | U | U | U | A | 30 | 4 | 15 | bc | false | <90% | 1623 | ||
NM_198514 | NHLRC2 | 2299 | 2317 | G | u | A | U | G | A | u | G | A | A | G | G | C | A | A | U | U | U | u | 17 | 3 | 11 | bc | false | <90% | 2550 | ||
XM_001131946 | LOC730359 | 691 | 709 | G | G | A | U | G | A | a | G | A | A | G | G | C | u | A | U | U | U | c | 9 | 3 | 6 | c | false | <90% | 1694 | ||
XM_001131663 | LOC729890 | 691 | 709 | G | G | A | U | G | A | a | G | A | A | G | G | C | u | A | U | U | U | c | 9 | 3 | 6 | c | false | <90% | 1694 | ||
XM_001126540 | LOC730608 | 691 | 709 | G | G | A | U | G | A | a | G | A | A | G | G | C | u | A | U | U | U | c | 9 | 3 | 6 | c | false | <90% | 1694 | ||
NM_003670 | BHLHB2 | 1081 | 1099 | G | G | A | U | G | A | u | G | A | A | G | G | C | c | A | U | U | U | c | 9 | 3 | 6 | c | false | <90% | 2922 | ||
NM_024560 | FLJ21963 | 1720 | 1738 | G | G | A | U | G | A | a | G | A | A | G | G | C | u | A | U | U | U | g | 9 | 3 | 6 | c | false | <90% | 3033 | ||
NM_001936 | DPP6 | 2777 | 2795 | G | G | A | U | G | c | G | G | A | A | G | G | C | A | g | U | U | U | u | 7 | 3 | 8 | c | false | <90% | 4460 | ||
NM_130797 | DPP6 | 2859 | 2877 | G | G | A | U | G | c | G | G | A | A | G | G | C | A | g | U | U | U | u | 7 | 3 | 8 | c | false | <90% | 4542 | ||
NM_001039350 | DPP6 | 2888 | 2906 | G | G | A | U | G | c | G | G | A | A | G | G | C | A | g | U | U | U | u | 7 | 3 | 8 | c | false | <90% | 4571 | ||
NM_000552 | VWF | 2275 | 2293 | G | G | A | U | G | A | G | G | A | A | u | G | C | A | A | U | g | a | g | 7 | 4 | 10 | c | false | <90% | 8833 | ||
NM_003170 | SUPT6H | 234 | 252 | G | G | A | U | G | A | G | c | A | A | G | G | C | A | A | c | U | U | g | 6 | 3 | 7 | c | false | <90% | 5896 | ||
NM_005572 | LMNA | 1547 | 1565 | G | G | A | U | G | A | G | G | A | g | G | G | C | A | A | g | U | U | u | -13 | 3 | 9 | c | false | <90% | 2032 | ||
NM_170708 | LMNA | 1547 | 1565 | G | G | A | U | G | A | G | G | A | g | G | G | C | A | A | g | U | U | u | -13 | 3 | 9 | c | false | <90% | 3091 | ||
NM_170707 | LMNA | 1547 | 1565 | G | G | A | U | G | A | G | G | A | g | G | G | C | A | A | g | U | U | u | -13 | 3 | 9 | c | false | <90% | 3181 |
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_152133 | TAGAP | 3166 | 3184 | U | A | A | A | U | U | G | C | C | U | U | C | C | U | u | A | U | u | u | 67 | 3 | 14 | c | false | <90% | 3196 | ||
NM_054114 | TAGAP | 3333 | 3351 | U | A | A | A | U | U | G | C | C | U | U | C | C | U | u | A | U | u | u | 67 | 3 | 14 | c | false | <90% | 3363 | ||
NM_004797 | ADIPOQ | 1326 | 1344 | g | A | A | u | U | U | G | C | C | U | U | C | C | U | C | A | U | g | a | 53 | 4 | 13 | c | false | <90% | 4592 | ||
NM_002308 | LGALS9 | 1279 | 1297 | g | g | g | A | U | U | G | C | C | U | U | C | C | U | C | A | g | C | C | 43 | 4 | 13 | c | false | <90% | 1739 | ||
NM_001040078 | LOC654346 | 1330 | 1348 | g | g | g | A | U | U | G | C | C | U | U | C | C | U | C | A | g | C | C | 43 | 4 | 13 | c | false | <90% | 1743 | ||
NM_009587 | LGALS9 | 1375 | 1393 | g | g | g | A | U | U | G | C | C | U | U | C | C | U | C | A | g | C | C | 43 | 4 | 13 | c | false | <90% | 1835 | ||
NM_015470 | RAB11FIP5 | 2199 | 2217 | c | A | A | A | U | a | G | C | C | U | U | C | C | U | C | A | c | C | C | 11 | 3 | 10 | c | false | <90% | 4362 | ||
NM_001018058 | TFEC | 4848 | 4866 | g | A | A | A | U | a | G | C | C | U | U | C | C | U | C | u | U | C | C | 8 | 3 | 9 | c | false | <90% | 6544 | ||
NM_012252 | TFEC | 4935 | 4953 | g | A | A | A | U | a | G | C | C | U | U | C | C | U | C | u | U | C | C | 8 | 3 | 9 | c | false | <90% | 6631 |
3 prime UTR Seed matches
Hits to same gene : 0
Hits to other genes : 1823
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