Automatic recommendation
OK - siRNA is specific for both sense and antisense (guide) strands
20 hits were found for GAUGGAGAGCCUUGUUCUU (6 guide strand hits and 14 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_001010922 | C1orf178 | 296 | 314 | u | c | a | G | G | A | G | A | G | C | C | U | U | G | U | U | C | U | U | 67 | 3 | 16 | bc | false | <90% | 4986 | ||
| NM_017622 | C17orf59 | 1493 | 1511 | G | A | U | G | G | A | G | A | G | C | C | U | U | c | U | g | C | U | U | 54 | 2 | 13 | c | false | <90% | 1758 | ||
| NM_052916 | RNF157 | 3333 | 3351 | G | A | U | G | G | A | G | A | G | C | C | U | U | G | a | g | C | U | a | 44 | 3 | 14 | c | false | <90% | 3570 | ||
| NM_002501 | NFIX | 923 | 941 | G | A | U | G | G | A | G | A | G | C | C | c | U | G | U | U | g | a | U | 40 | 3 | 11 | false | <90% | 5576 | |||
| NM_020340 | KIAA1244 | 3695 | 3713 | G | A | U | G | G | A | G | A | c | C | C | U | U | G | U | U | C | a | g | 32 | 3 | 8 | c | false | <90% | 8658 | ||
| NM_005733 | KIF20A | 303 | 321 | u | g | U | G | G | A | G | A | c | C | C | U | U | G | U | U | C | U | a | 21 | 4 | 9 | bc | false | <90% | 2972 | ||
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_032010 | MAP1B | 4268 | 4286 | g | A | a | A | A | C | A | A | G | G | C | U | C | U | C | C | A | g | a | 70 | 4 | 14 | c | false | <90% | 9161 | ||
| NM_005909 | MAP1B | 4523 | 4541 | g | A | a | A | A | C | A | A | G | G | C | U | C | U | C | C | A | g | a | 70 | 4 | 14 | c | false | <90% | 9416 | ||
| NM_017533 | MYH4 | 3106 | 3124 | g | A | G | A | A | g | A | A | G | G | C | U | C | U | C | C | A | g | g | 27 | 4 | 11 | c | false | <90% | 6016 | ||
| NM_002472 | MYH8 | 3065 | 3083 | g | A | G | A | A | g | A | A | G | G | C | U | C | U | C | C | A | a | g | 27 | 4 | 11 | c | false | <90% | 6016 | ||
| NM_005963 | MYH1 | 3089 | 3107 | g | A | G | A | A | g | A | A | G | G | C | U | C | U | C | C | A | g | g | 27 | 4 | 11 | c | false | <90% | 6038 | ||
| NM_017534 | MYH2 | 3091 | 3109 | g | A | G | A | A | g | A | A | G | G | C | U | C | U | C | C | A | g | g | 27 | 4 | 11 | c | false | <90% | 6061 | ||
| NM_181489 | ZNF445 | 5673 | 5691 | u | u | u | A | c | C | A | A | G | G | C | U | C | U | C | C | A | U | C | 15 | 4 | 14 | bc | false | <90% | 9105 | ||
| NM_004543 | NEB | 9783 | 9801 | A | A | G | A | A | C | A | A | u | G | C | U | C | U | C | a | A | U | a | 8 | 3 | 8 | c | false | <90% | 20632 | ||
| NM_213633 | PSG4 | 1335 | 1353 | c | A | G | A | A | C | A | A | G | a | C | U | C | c | C | C | A | U | C | -4 | 3 | 8 | c | false | <90% | 1780 | ||
| NM_002780 | PSG4 | 1614 | 1632 | c | A | G | A | A | C | A | A | G | a | C | U | C | c | C | C | A | U | C | -4 | 3 | 8 | c | false | <90% | 2059 | ||
| NM_001040453 | FAM63B | 1949 | 1967 | c | A | G | c | A | C | A | A | G | c | C | U | C | U | C | C | A | U | C | -21 | 3 | 9 | bc | false | <90% | 5010 | ||
| NM_001040450 | FAM63B | 1952 | 1970 | c | A | G | c | A | C | A | A | G | c | C | U | C | U | C | C | A | U | C | -21 | 3 | 9 | bc | false | <90% | 5013 | ||
| NM_133482 | RAD50 | 5164 | 5182 | A | A | G | A | A | C | A | g | G | c | C | U | C | U | C | C | A | U | u | -49 | 3 | 8 | bc | false | <90% | 5826 | ||
| NM_005732 | RAD50 | 5229 | 5247 | A | A | G | A | A | C | A | g | G | c | C | U | C | U | C | C | A | U | u | -49 | 3 | 8 | bc | false | <90% | 5891 | ||
3 prime UTR Seed matches
Hits to same gene : 0
Hits to other genes : 2567
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