Automatic recommendation
Not OK - siRNA is not specific
15 hits were found for GGACCGACAUUGUGGAGGU (13 guide strand hits and 2 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_014866 | KIAA0310 | 4967 | 4985 | G | G | A | C | C | G | A | C | A | U | U | G | c | G | G | A | G | c | U | 86 | 2 | 12 | false | <90% | 9059 | |||
NM_001556 | IKBKB | 1799 | 1817 | a | G | A | C | C | G | A | C | A | U | U | G | U | G | G | A | c | u | U | 71 | 3 | 15 | ac | false | <90% | 3916 | ||
NM_001017423 | ALDH18A1 | 1255 | 1273 | u | c | A | C | a | G | A | C | A | U | U | G | U | G | G | A | G | G | g | 30 | 4 | 13 | bc | false | <90% | 3464 | ||
NM_002860 | ALDH18A1 | 1261 | 1279 | u | c | A | C | a | G | A | C | A | U | U | G | U | G | G | A | G | G | g | 30 | 4 | 13 | bc | false | <90% | 3470 | ||
NM_003866 | INPP4B | 360 | 378 | G | c | A | C | C | G | A | a | A | U | U | G | U | G | G | A | G | G | g | 21 | 3 | 10 | bc | false | <90% | 2937 | ||
NM_030819 | GFOD2 | 784 | 802 | G | G | A | C | C | u | A | C | A | U | U | G | U | G | G | A | c | c | U | 10 | 3 | 10 | c | false | <90% | 2118 | ||
XM_046531 | KIAA1614 | 1920 | 1938 | G | G | A | C | C | G | A | C | A | g | U | G | a | G | G | A | G | G | c | 1 | 3 | 9 | false | <90% | 6999 | |||
XM_942569 | KIAA1614 | 1920 | 1938 | G | G | A | C | C | G | A | C | A | g | U | G | a | G | G | A | G | G | c | 1 | 3 | 9 | false | <90% | 7000 | |||
XM_378080 | LOC402377 | 560 | 578 | G | G | A | C | u | G | A | C | u | U | U | G | U | G | G | A | G | G | a | -16 | 3 | 9 | bc | false | <90% | 1275 | ||
XM_936890 | LOC402377 | 560 | 578 | G | G | A | C | u | G | A | C | u | U | U | G | U | G | G | A | G | G | a | -16 | 3 | 9 | bc | false | <90% | 1275 | ||
NM_002332 | LRP1 | 4404 | 4422 | G | G | A | C | C | G | A | C | g | U | g | G | U | G | G | A | G | G | a | -26 | 3 | 8 | c | false | <90% | 14905 | ||
NM_002020 | FLT4 | 1575 | 1593 | G | G | A | C | C | G | A | g | u | U | U | G | U | G | G | A | G | G | g | -27 | 3 | 9 | bc | false | <90% | 4510 | ||
NM_182925 | FLT4 | 1575 | 1593 | G | G | A | C | C | G | A | g | u | U | U | G | U | G | G | A | G | G | g | -27 | 3 | 9 | bc | false | <90% | 5833 |
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_021245 | MYOZ1 | 357 | 375 | A | C | C | U | C | C | A | C | A | A | U | G | c | C | G | c | U | C | u | 58 | 3 | 12 | false | <90% | 1661 | |||
NM_003236 | TGFA | 1787 | 1805 | A | C | C | U | C | C | A | C | u | A | U | G | U | g | G | G | U | C | u | 15 | 3 | 8 | c | false | <90% | 4119 |
3 prime UTR Seed matches
Hits to same gene : 0
Hits to other genes : 318
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