Automatic recommendation
OK - siRNA is specific for both sense and antisense (guide) strands
20 hits were found for GAAGCAGAGCCAUUUGGUU (11 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_002253 | KDR | 1524 | 1542 | G | A | A | G | C | A | G | A | G | C | C | A | U | g | U | G | G | U | c | 75 | 2 | 13 | c | false | <90% | 5830 | ||
NM_138300 | PYGO2 | 1667 | 1685 | u | g | A | G | C | A | G | A | G | C | C | A | U | U | U | u | G | U | g | 55 | 4 | 13 | c | false | <90% | 3227 | ||
NM_000236 | LIPC | 139 | 157 | a | A | A | c | C | A | G | A | G | C | C | A | U | U | U | G | G | a | a | 53 | 4 | 13 | c | false | <90% | 1603 | ||
XM_495886 | RNF169 | 3950 | 3968 | a | A | A | G | C | A | G | A | G | C | C | A | U | U | U | u | c | U | U | 48 | 3 | 14 | c | false | <90% | 8900 | ||
XM_940188 | RNF169 | 3950 | 3968 | a | A | A | G | C | A | G | A | G | C | C | A | U | U | U | u | c | U | U | 48 | 3 | 14 | c | false | <90% | 8900 | ||
NM_181707 | C17orf64 | 324 | 342 | G | A | A | G | C | A | G | A | G | C | C | u | U | g | U | G | G | U | c | 41 | 3 | 11 | false | <90% | 971 | |||
NM_001279 | CIDEA | 938 | 956 | G | u | g | u | C | A | G | A | G | C | C | A | U | U | U | G | G | U | c | 27 | 4 | 14 | bc | false | <90% | 996 | ||
NM_198289 | CIDEA | 1055 | 1073 | G | u | g | u | C | A | G | A | G | C | C | A | U | U | U | G | G | U | c | 27 | 4 | 14 | bc | false | <90% | 1113 | ||
XR_019466 | LOC649728 | 1249 | 1267 | G | u | g | u | C | A | G | A | G | C | C | A | U | U | U | G | G | U | c | 27 | 4 | 14 | bc | false | <90% | 1307 | ||
NM_006750 | SNTB2 | 4055 | 4073 | G | c | A | G | C | A | a | A | G | C | C | A | U | U | U | G | G | U | U | 22 | 2 | 12 | bc | false | <90% | 9771 | ||
NM_030579 | CYB5B | 3965 | 3983 | G | A | A | G | C | A | G | A | G | g | C | A | U | U | U | G | u | c | a | -13 | 4 | 9 | c | false | <90% | 4286 |
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_014672 | KIAA0391 | 2080 | 2098 | A | A | C | C | A | A | A | U | G | G | C | U | u | U | G | C | c | U | C | 66 | 2 | 12 | false | <90% | 2684 | |||
NM_016953 | PDE11A | 547 | 565 | g | A | C | C | A | A | A | U | G | G | C | U | C | U | G | C | c | c | a | 66 | 4 | 15 | ac | false | <90% | 9285 | ||
NM_021190 | PTBP2 | 1525 | 1543 | c | A | C | a | A | A | A | U | G | G | C | U | C | U | u | C | U | U | C | 36 | 3 | 10 | c | false | <90% | 3054 | ||
NM_020158 | EXOSC5 | 145 | 163 | g | g | C | C | A | g | A | U | G | G | C | U | C | U | G | C | U | U | C | 23 | 3 | 13 | bc | false | <90% | 1006 | ||
NM_001012642 | GRAMD2 | 341 | 359 | c | c | C | C | A | A | c | U | G | G | C | U | C | U | G | C | U | U | C | 20 | 3 | 12 | bc | false | <90% | 3280 | ||
NM_212558 | LOC401498 | 1132 | 1150 | A | A | g | C | A | A | A | U | u | G | C | U | C | U | G | C | U | U | g | 15 | 3 | 9 | bc | false | <90% | 3581 | ||
NM_002790 | PSMA5 | 590 | 608 | g | A | g | C | A | A | u | U | G | G | C | U | C | U | G | C | U | U | C | 12 | 3 | 12 | bc | false | <90% | 1023 | ||
NM_024091 | FASTKD3 | 1403 | 1421 | c | A | C | C | A | A | A | U | G | c | C | U | C | U | G | C | U | U | u | 10 | 3 | 8 | bc | false | <90% | 2416 | ||
NM_000819 | GART | 2574 | 2592 | A | A | C | C | A | A | A | U | a | G | C | U | C | U | G | C | a | c | a | 8 | 4 | 8 | c | false | <90% | 3300 |
3 prime UTR Seed matches
Hits to same gene : 0
Hits to other genes : 3225
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