Automatic recommendation
OK - siRNA is specific for both sense and antisense (guide) strands
22 hits were found for ACUUCGCUUCACCUCUGCA (5 guide strand hits and 17 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 | |||||||||||||
| XM_001126826 | LOC730695 | 432 | 450 | c | u | U | a | C | G | C | U | U | C | A | C | C | U | C | U | G | C | c | 44 | 4 | 14 | bc | false | <90% | 507 | ||
| NM_130839 | UBE3A | 151 | 169 | c | u | U | a | C | G | C | U | U | C | A | C | C | U | C | U | G | C | c | 44 | 4 | 14 | bc | false | <90% | 5164 | ||
| NM_005113 | GOLGA5 | 2298 | 2316 | g | C | U | U | u | G | C | U | U | C | A | C | C | U | C | U | G | g | g | 38 | 4 | 12 | c | false | <90% | 2891 | ||
| NM_006923 | SDF2 | 359 | 377 | A | C | U | U | C | a | C | U | U | C | A | C | C | U | C | U | u | u | c | 5 | 4 | 10 | c | false | <90% | 1075 | ||
| NM_004849 | ATG5 | 1352 | 1370 | A | C | U | U | u | G | C | a | U | C | A | C | C | U | C | U | G | C | u | -18 | 3 | 10 | bc | false | <90% | 3244 | ||
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_001080142 | CT47.5 | 1128 | 1146 | a | G | C | A | G | A | G | G | U | G | A | A | G | C | c | A | A | G | a | 68 | 3 | 13 | c | false | <90% | 1294 | ||
| NM_001080141 | CT47.6 | 1128 | 1146 | a | G | C | A | G | A | G | G | U | G | A | A | G | C | c | A | A | G | a | 68 | 3 | 13 | c | false | <90% | 1294 | ||
| NM_001080143 | CT47.4 | 1128 | 1146 | a | G | C | A | G | A | G | G | U | G | A | A | G | C | c | A | A | G | a | 68 | 3 | 13 | c | false | <90% | 1294 | ||
| NM_001080138 | CT47.9 | 1128 | 1146 | a | G | C | A | G | A | G | G | U | G | A | A | G | C | c | A | A | G | a | 68 | 3 | 13 | c | false | <90% | 1294 | ||
| NM_001080144 | CT47.3 | 1128 | 1146 | a | G | C | A | G | A | G | G | U | G | A | A | G | C | c | A | A | G | a | 68 | 3 | 13 | c | false | <90% | 1294 | ||
| NM_001080137 | CT47.10 | 1128 | 1146 | a | G | C | A | G | A | G | G | U | G | A | A | G | C | c | A | A | G | a | 68 | 3 | 13 | c | false | <90% | 1294 | ||
| NM_001080139 | CT47.8 | 1128 | 1146 | a | G | C | A | G | A | G | G | U | G | A | A | G | C | c | A | A | G | a | 68 | 3 | 13 | c | false | <90% | 1294 | ||
| NM_001080140 | CT47.7 | 1128 | 1146 | a | G | C | A | G | A | G | G | U | G | A | A | G | C | c | A | A | G | a | 68 | 3 | 13 | c | false | <90% | 1294 | ||
| NM_001080146 | CT47.1 | 1128 | 1146 | a | G | C | A | G | A | G | G | U | G | A | A | G | C | c | A | A | G | a | 68 | 3 | 13 | c | false | <90% | 1294 | ||
| NM_001080145 | CT47.2 | 1128 | 1146 | a | G | C | A | G | A | G | G | U | G | A | A | G | C | c | A | A | G | a | 68 | 3 | 13 | c | false | <90% | 1294 | ||
| NM_173571 | CT47.11 | 1128 | 1146 | a | G | C | A | G | A | G | G | U | G | A | A | G | C | c | A | A | G | a | 68 | 3 | 13 | c | false | <90% | 1294 | ||
| NM_014374 | REPIN1 | 2280 | 2298 | g | c | a | A | G | A | G | G | U | G | A | A | G | C | G | A | A | G | c | 62 | 4 | 15 | bc | false | <90% | 2873 | ||
| NM_013400 | REPIN1 | 2332 | 2350 | g | c | a | A | G | A | G | G | U | G | A | A | G | C | G | A | A | G | c | 62 | 4 | 15 | bc | false | <90% | 2952 | ||
| XR_018231 | LOC648027 | 361 | 379 | g | G | C | A | G | A | G | G | U | G | A | g | G | C | G | A | A | u | U | 61 | 3 | 10 | false | <90% | 1255 | |||
| XR_016969 | LOC391698 | 361 | 379 | g | G | C | A | G | A | G | G | U | G | A | g | G | C | G | A | A | u | U | 61 | 3 | 10 | false | <90% | 1255 | |||
| NM_004335 | BST2 | 400 | 418 | U | G | C | A | G | A | G | G | U | G | g | A | G | C | G | A | c | u | g | 7 | 4 | 10 | c | false | <90% | 983 | ||
| NM_007192 | SUPT16H | 1746 | 1764 | U | G | C | A | G | A | a | G | a | G | A | A | G | C | G | A | A | G | a | -31 | 3 | 9 | bc | false | <90% | 4696 | ||
3 prime UTR Seed matches
Hits to same gene : 0
Hits to other genes : 0
View matched accessions
3 prime seed match details
| Accession | Gene name | Hits to this gene |
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