Automatic recommendation
OK - siRNA is specific for both sense and antisense (guide) strands
14 hits were found for CUCCCAAUAUCCAUCUGCU (7 guide strand hits and 7 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_145213 | MRPL30 | 872 | 890 | g | U | C | C | C | A | A | U | A | U | C | C | A | U | C | c | u | g | U | 45 | 4 | 14 | c | false | <90% | 1172 | ||
| NM_001010888 | ZC3H12B | 1859 | 1877 | C | U | C | C | C | A | A | U | A | U | C | C | A | U | C | c | u | g | g | 42 | 4 | 15 | c | false | <90% | 7024 | ||
| NM_152430 | OR51E1 | 1030 | 1048 | u | g | g | C | C | A | A | U | A | U | C | u | A | U | C | U | G | C | U | 33 | 4 | 8 | false | <90% | 1350 | |||
| NM_007131 | ZNF75 | 2228 | 2246 | C | U | u | C | C | A | A | g | A | U | C | C | A | U | C | U | G | C | c | 13 | 3 | 10 | bc | false | <90% | 5583 | ||
| NM_015278 | SASH1 | 2915 | 2933 | C | U | C | C | C | A | g | U | u | U | C | C | A | U | C | U | G | C | c | -31 | 3 | 9 | bc | false | <90% | 7709 | ||
| NM_001043318 | C14orf43 | 6754 | 6772 | C | U | C | C | C | A | g | c | A | U | C | C | A | U | C | U | G | C | a | -33 | 3 | 10 | bc | false | <90% | 7656 | ||
| NM_194278 | C14orf43 | 7198 | 7216 | C | U | C | C | C | A | g | c | A | U | C | C | A | U | C | U | G | C | a | -33 | 3 | 10 | bc | false | <90% | 8100 | ||
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_153331 | KCTD6 | 385 | 403 | A | G | C | A | G | A | U | G | G | A | U | A | a | U | G | G | a | g | a | 58 | 4 | 12 | false | <90% | 1823 | |||
| NM_032997 | ZWINT | 1012 | 1030 | A | G | C | A | G | A | U | G | G | A | U | g | g | U | G | G | G | A | a | 50 | 3 | 11 | false | <90% | 1878 | |||
| XM_001125745 | ZNF469 | 5850 | 5868 | g | G | C | A | G | A | U | G | G | A | c | A | U | U | G | G | G | g | c | 29 | 4 | 9 | c | false | <90% | 13203 | ||
| XM_939259 | ZNF469 | 5850 | 5868 | g | G | C | A | G | A | U | G | G | A | c | A | U | U | G | G | G | g | c | 29 | 4 | 9 | c | false | <90% | 13229 | ||
| NR_003366 | ANKRD20B | 94414 | 94432 | g | G | C | A | G | g | U | G | c | A | U | A | U | U | G | G | G | A | G | -25 | 3 | 10 | bc | false | <90% | 96524 | ||
| NM_015197 | PACS2 | 1497 | 1515 | c | G | C | A | G | A | c | G | G | A | g | A | U | U | G | G | G | A | G | -29 | 3 | 8 | c | false | <90% | 3173 | ||
| NM_182526 | C14orf83 | 1117 | 1135 | A | G | C | A | G | A | g | G | G | A | c | A | U | U | G | G | G | A | a | -32 | 3 | 7 | c | false | <90% | 4068 | ||
3 prime UTR Seed matches
Hits to same gene : 0
Hits to other genes : 3592
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