Automatic recommendation
OK - siRNA is specific for both sense and antisense (guide) strands
11 hits were found for CCCAUUACAAUAUUGUAAC (3 guide strand hits and 8 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_014940 | MON1B | 3244 | 3262 | C | C | C | A | U | U | A | C | A | A | U | A | a | U | G | a | A | A | u | 58 | 3 | 12 | false | <90% | 3328 | |||
| NM_004898 | CLOCK | 4444 | 4462 | a | a | C | A | U | U | A | g | A | A | U | A | U | U | G | U | A | A | C | 24 | 3 | 11 | bc | false | <90% | 5801 | ||
| NM_005284 | GPR6 | 1609 | 1627 | C | C | C | A | U | U | A | C | A | A | g | A | a | U | G | U | A | A | a | 23 | 3 | 10 | false | <90% | 1645 | |||
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_006888 | CALM1 | 3579 | 3597 | G | U | a | A | C | A | A | U | A | U | U | G | U | A | A | U | G | a | a | 72 | 3 | 14 | c | false | <90% | 4201 | ||
| NM_001002918 | OR8D2 | 392 | 410 | u | U | U | A | C | A | A | U | A | U | U | G | U | c | A | U | G | u | c | 70 | 4 | 12 | c | false | <90% | 936 | ||
| NM_006726 | LRBA | 9211 | 9229 | G | U | U | A | C | A | A | U | A | U | U | G | g | A | A | U | a | G | G | 66 | 2 | 12 | false | <90% | 9909 | |||
| NM_007270 | FKBP9 | 1380 | 1398 | c | U | U | A | C | A | A | U | A | U | U | G | U | u | c | U | G | G | G | 53 | 3 | 12 | c | false | <90% | 3425 | ||
| NR_003366 | ANKRD20B | 30325 | 30343 | c | a | c | A | C | A | A | U | A | U | U | G | U | c | A | U | G | G | G | 47 | 4 | 10 | c | false | <90% | 96524 | ||
| NM_016097 | IER3IP1 | 1402 | 1420 | G | U | U | A | C | A | A | U | A | U | U | u | U | A | A | a | G | G | u | 35 | 3 | 11 | false | <90% | 1491 | |||
| NM_148174 | AZIN1 | 4020 | 4038 | G | U | U | A | u | A | A | U | A | U | U | G | U | A | A | U | c | u | c | 17 | 4 | 11 | c | false | <90% | 4202 | ||
| NM_015878 | AZIN1 | 4166 | 4184 | G | U | U | A | u | A | A | U | A | U | U | G | U | A | A | U | c | u | c | 17 | 4 | 11 | c | false | <90% | 4348 | ||
3 prime UTR Seed matches
Hits to same gene : 0
Hits to other genes : 1239
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