Automatic recommendation
OK - siRNA is specific for both sense and antisense (guide) strands
22 hits were found for AGAGAUGGUGUCCGGAGAC (17 guide strand hits and 5 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_177452 | TRAPPC6B | 371 | 389 | c | G | A | G | A | U | G | G | U | G | U | C | u | G | G | A | G | u | g | 79 | 4 | 11 | false | <90% | 3280 | |||
NM_001079537 | TRAPPC6B | 371 | 389 | c | G | A | G | A | U | G | G | U | G | U | C | u | G | G | A | G | u | g | 79 | 4 | 11 | false | <90% | 3364 | |||
NM_080679 | COL11A2 | 358 | 376 | c | c | u | G | A | U | G | G | U | G | U | C | C | G | G | A | G | A | g | 62 | 4 | 15 | bc | false | <90% | 6104 | ||
NM_080681 | COL11A2 | 358 | 376 | c | c | u | G | A | U | G | G | U | G | U | C | C | G | G | A | G | A | g | 62 | 4 | 15 | bc | false | <90% | 6167 | ||
NM_080680 | COL11A2 | 358 | 376 | c | c | u | G | A | U | G | G | U | G | U | C | C | G | G | A | G | A | g | 62 | 4 | 15 | bc | false | <90% | 6425 | ||
NM_153442 | GPR26 | 7241 | 7259 | A | G | A | G | A | U | G | G | U | G | U | C | a | G | G | u | G | A | g | 58 | 3 | 12 | false | <90% | 7512 | |||
NM_170719 | C13orf23 | 4728 | 4746 | A | a | A | G | A | U | G | G | U | G | U | C | C | G | G | A | a | g | a | 57 | 4 | 14 | ac | false | <90% | 5162 | ||
NM_025138 | C13orf23 | 4794 | 4812 | A | a | A | G | A | U | G | G | U | G | U | C | C | G | G | A | a | g | a | 57 | 4 | 14 | ac | false | <90% | 5228 | ||
NM_015030 | FRYL | 11393 | 11411 | A | G | g | G | A | U | G | G | U | G | U | C | C | a | G | A | G | A | u | 55 | 3 | 10 | c | false | <90% | 11706 | ||
NM_178518 | TMEM102 | 714 | 732 | A | G | A | G | A | U | G | G | U | G | U | g | C | G | G | A | a | c | C | 40 | 3 | 11 | false | <90% | 1996 | |||
NM_173832 | ZFP41 | 439 | 457 | g | G | A | G | A | a | G | G | U | G | U | C | C | G | G | g | G | A | C | 8 | 3 | 9 | c | false | <90% | 4786 | ||
NM_004433 | ELF3 | 3040 | 3058 | A | G | A | G | A | g | G | G | U | G | U | C | C | G | c | A | G | A | g | 7 | 3 | 8 | c | false | <90% | 5036 | ||
NM_019021 | C11orf71 | 279 | 297 | g | G | c | G | A | U | G | G | U | c | U | C | C | G | G | A | G | A | C | -4 | 3 | 9 | bc | false | <90% | 1466 | ||
NM_198082 | CCDC57 | 1153 | 1171 | g | G | A | G | A | U | G | G | U | c | U | C | C | a | G | A | G | A | C | -4 | 3 | 8 | c | false | <90% | 2997 | ||
NM_001191 | BCL2L1 | 2175 | 2193 | A | G | A | G | c | U | G | G | U | G | c | C | C | G | G | A | G | A | u | -17 | 3 | 7 | c | false | <90% | 2386 | ||
NM_138578 | BCL2L1 | 2364 | 2382 | A | G | A | G | c | U | G | G | U | G | c | C | C | G | G | A | G | A | u | -17 | 3 | 7 | c | false | <90% | 2575 | ||
NM_019116 | UBFD1 | 3766 | 3784 | A | G | A | G | c | U | G | G | U | u | U | C | C | G | G | A | G | A | g | -39 | 3 | 8 | bc | false | <90% | 4931 |
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_181537 | KRT27 | 30 | 48 | G | c | C | U | C | C | G | G | A | C | A | C | C | A | U | g | U | C | U | 62 | 2 | 13 | c | false | <90% | 1635 | ||
NM_001035235 | SRA1 | 1335 | 1353 | c | U | C | a | C | C | G | G | A | C | A | C | C | A | U | C | U | C | c | 56 | 3 | 14 | bc | false | <90% | 1965 | ||
NM_021933 | IIP45 | 730 | 748 | G | U | C | U | C | u | G | G | A | C | A | C | C | A | g | C | U | C | U | 12 | 2 | 8 | c | false | <90% | 1588 | ||
NM_130760 | MADCAM1 | 727 | 745 | G | U | C | U | C | C | c | G | A | C | A | C | C | A | c | C | U | C | c | 4 | 3 | 7 | c | false | <90% | 1546 | ||
NM_130760 | MADCAM1 | 751 | 769 | G | U | C | U | C | C | c | G | A | C | A | C | C | A | c | C | U | C | c | 4 | 3 | 7 | c | false | <90% | 1546 |
3 prime UTR Seed matches
Hits to same gene : 0
Hits to other genes : 3417
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