Automatic recommendation
OK - siRNA is specific for both sense and antisense (guide) strands
22 hits were found for GCACUUCGCUUCACCUCUG (4 guide strand hits and 18 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_001040455 | SIDT2 | 2551 | 2569 | G | C | c | C | U | U | C | G | C | U | U | C | A | C | C | U | C | a | a | 72 | 3 | 14 | c | false | <90% | 3919 | ||
| NM_006923 | SDF2 | 357 | 375 | c | C | A | C | U | U | C | a | C | U | U | C | A | C | C | U | C | U | u | 30 | 3 | 10 | bc | false | <90% | 1075 | ||
| NM_005113 | GOLGA5 | 2296 | 2314 | u | g | g | C | U | U | u | G | C | U | U | C | A | C | C | U | C | U | G | 0 | 4 | 12 | bc | false | <90% | 2891 | ||
| NM_005912 | MC4R | 448 | 466 | a | C | A | C | U | U | C | u | C | U | g | C | A | C | C | U | C | U | G | -25 | 3 | 8 | c | false | <90% | 1438 | ||
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_014374 | REPIN1 | 2278 | 2296 | a | A | G | A | G | G | U | G | A | A | G | C | G | A | A | G | c | c | a | 66 | 4 | 15 | ac | false | <90% | 2873 | ||
| NM_013400 | REPIN1 | 2330 | 2348 | a | A | G | A | G | G | U | G | A | A | G | C | G | A | A | G | c | c | a | 66 | 4 | 15 | ac | false | <90% | 2952 | ||
| NM_001080142 | CT47.5 | 1127 | 1145 | C | A | G | A | G | G | U | G | A | A | G | C | c | A | A | G | a | a | a | 58 | 4 | 12 | false | <90% | 1294 | |||
| NM_001080141 | CT47.6 | 1127 | 1145 | C | A | G | A | G | G | U | G | A | A | G | C | c | A | A | G | a | a | a | 58 | 4 | 12 | false | <90% | 1294 | |||
| NM_001080143 | CT47.4 | 1127 | 1145 | C | A | G | A | G | G | U | G | A | A | G | C | c | A | A | G | a | a | a | 58 | 4 | 12 | false | <90% | 1294 | |||
| NM_001080138 | CT47.9 | 1127 | 1145 | C | A | G | A | G | G | U | G | A | A | G | C | c | A | A | G | a | a | a | 58 | 4 | 12 | false | <90% | 1294 | |||
| NM_001080144 | CT47.3 | 1127 | 1145 | C | A | G | A | G | G | U | G | A | A | G | C | c | A | A | G | a | a | a | 58 | 4 | 12 | false | <90% | 1294 | |||
| NM_001080137 | CT47.10 | 1127 | 1145 | C | A | G | A | G | G | U | G | A | A | G | C | c | A | A | G | a | a | a | 58 | 4 | 12 | false | <90% | 1294 | |||
| NM_001080139 | CT47.8 | 1127 | 1145 | C | A | G | A | G | G | U | G | A | A | G | C | c | A | A | G | a | a | a | 58 | 4 | 12 | false | <90% | 1294 | |||
| NM_001080140 | CT47.7 | 1127 | 1145 | C | A | G | A | G | G | U | G | A | A | G | C | c | A | A | G | a | a | a | 58 | 4 | 12 | false | <90% | 1294 | |||
| NM_001080146 | CT47.1 | 1127 | 1145 | C | A | G | A | G | G | U | G | A | A | G | C | c | A | A | G | a | a | a | 58 | 4 | 12 | false | <90% | 1294 | |||
| NM_001080145 | CT47.2 | 1127 | 1145 | C | A | G | A | G | G | U | G | A | A | G | C | c | A | A | G | a | a | a | 58 | 4 | 12 | false | <90% | 1294 | |||
| NM_173571 | CT47.11 | 1127 | 1145 | C | A | G | A | G | G | U | G | A | A | G | C | c | A | A | G | a | a | a | 58 | 4 | 12 | false | <90% | 1294 | |||
| NM_003486 | SLC7A5 | 2968 | 2986 | C | A | G | A | G | G | U | G | g | A | G | C | c | A | A | G | U | G | g | 24 | 3 | 8 | false | <90% | 4543 | |||
| NM_001033087 | C20orf133 | 545 | 563 | C | A | G | A | G | G | a | G | A | A | G | C | a | A | A | G | U | G | u | 18 | 3 | 6 | false | <90% | 4425 | |||
| NM_080676 | C20orf133 | 1052 | 1070 | C | A | G | A | G | G | a | G | A | A | G | C | a | A | A | G | U | G | u | 18 | 3 | 6 | false | <90% | 4863 | |||
| NM_017823 | DUSP23 | 540 | 558 | C | A | G | A | G | a | U | G | A | A | G | g | G | A | A | G | U | G | g | -2 | 3 | 6 | false | <90% | 718 | |||
| NM_001839 | CNN3 | 187 | 205 | g | A | G | c | G | G | g | G | A | A | G | C | G | A | A | G | U | G | C | -5 | 3 | 12 | bc | false | <90% | 2045 | ||
3 prime UTR Seed matches
Hits to same gene : 0
Hits to other genes : 1588
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