Automatic recommendation
OK - siRNA is specific for both sense and antisense (guide) strands
20 hits were found for GGCUUGAGAGUGAAGUGAA (16 guide strand hits and 4 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_014516 | CNOT3 | 733 | 751 | a | G | u | U | U | G | A | G | A | G | U | G | A | A | G | U | G | g | A | 75 | 3 | 14 | c | false | <90% | 2855 | ||
| NM_017984 | ZCWPW1 | 1162 | 1180 | G | G | C | U | U | G | A | G | A | G | U | G | A | u | G | U | G | g | c | 72 | 3 | 13 | c | false | <90% | 2356 | ||
| NM_153366 | SVEP1 | 7007 | 7025 | u | c | u | U | U | G | A | G | A | G | U | G | A | A | G | U | G | A | g | 62 | 4 | 15 | bc | false | <90% | 11415 | ||
| NM_198881 | TBC1D8B | 104 | 122 | G | G | g | U | U | G | A | G | A | G | U | G | A | g | G | U | G | A | g | 55 | 3 | 10 | c | false | <90% | 2607 | ||
| NM_017752 | TBC1D8B | 104 | 122 | G | G | g | U | U | G | A | G | A | G | U | G | A | g | G | U | G | A | g | 55 | 3 | 10 | c | false | <90% | 5726 | ||
| NM_133280 | FCAR | 888 | 906 | G | c | a | c | U | G | A | G | A | G | U | G | A | A | G | U | G | A | A | 32 | 3 | 15 | bc | false | <90% | 1267 | ||
| NM_133279 | FCAR | 924 | 942 | G | c | a | c | U | G | A | G | A | G | U | G | A | A | G | U | G | A | A | 32 | 3 | 15 | bc | false | <90% | 1636 | ||
| NM_144684 | ZNF480 | 303 | 321 | c | u | g | g | U | G | A | G | A | G | U | G | A | A | G | U | G | A | A | 30 | 4 | 15 | bc | false | <90% | 4732 | ||
| NM_207311 | CCDC64 | 531 | 549 | a | G | C | U | g | G | A | G | A | G | U | G | A | u | G | U | G | A | A | 27 | 3 | 8 | c | false | <90% | 3081 | ||
| NM_001007239 | KIAA0859 | 1801 | 1819 | G | a | a | U | U | G | A | G | g | G | U | G | A | A | G | U | G | A | A | 8 | 3 | 10 | bc | false | <90% | 2953 | ||
| NM_014955 | KIAA0859 | 1944 | 1962 | G | a | a | U | U | G | A | G | g | G | U | G | A | A | G | U | G | A | A | 8 | 3 | 10 | bc | false | <90% | 3096 | ||
| NM_015935 | KIAA0859 | 2269 | 2287 | G | a | a | U | U | G | A | G | g | G | U | G | A | A | G | U | G | A | A | 8 | 3 | 10 | bc | false | <90% | 3421 | ||
| NM_001376 | DYNC1H1 | 13283 | 13301 | u | c | u | U | U | G | A | G | A | G | a | G | A | A | G | U | G | A | A | 5 | 4 | 8 | c | false | <90% | 14229 | ||
| NM_001042546 | ATPAF1 | 3141 | 3159 | G | G | C | U | U | u | A | G | A | G | U | u | A | A | G | U | G | A | A | 2 | 2 | 7 | false | <90% | 3936 | |||
| NM_022745 | ATPAF1 | 3345 | 3363 | G | G | C | U | U | u | A | G | A | G | U | u | A | A | G | U | G | A | A | 2 | 2 | 7 | false | <90% | 4140 | |||
| NM_020066 | FMN2 | 2558 | 2576 | G | G | C | U | U | G | A | G | A | a | U | G | g | A | G | U | G | A | c | 1 | 3 | 9 | false | <90% | 6644 | |||
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_152763 | C1orf62 | 1783 | 1801 | U | U | C | u | C | U | U | C | A | C | U | C | U | C | A | A | a | u | g | 32 | 4 | 12 | c | false | <90% | 3066 | ||
| NM_015196 | KIAA0922 | 2521 | 2539 | U | U | C | g | C | U | U | C | A | C | U | C | U | C | A | A | u | g | u | 32 | 4 | 12 | c | false | <90% | 4980 | ||
| NM_018558 | GABRQ | 1325 | 1343 | c | U | C | A | C | U | U | C | u | C | U | C | U | C | A | g | G | C | C | 11 | 3 | 7 | c | false | <90% | 2000 | ||
| NM_138357 | CCDC109A | 313 | 331 | g | U | C | A | g | U | U | C | A | C | a | C | U | C | A | A | G | C | C | -14 | 3 | 8 | c | false | <90% | 2978 | ||
3 prime UTR Seed matches
Hits to same gene : 0
Hits to other genes : 1570
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