Automatic recommendation
OK - siRNA is specific for both sense and antisense (guide) strands
15 hits were found for CCAGACACAUACUCCUCAG (8 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_019058 | DDIT4 | 1091 | 1109 | g | g | g | G | A | C | A | C | A | U | A | C | c | C | C | U | C | A | G | 56 | 4 | 9 | false | <90% | 1752 | |||
| NM_000163 | GHR | 3170 | 3188 | C | C | A | G | A | C | A | C | A | U | A | C | U | C | a | U | u | u | u | 44 | 4 | 14 | c | false | <90% | 4370 | ||
| NM_001080426 | DUSP27 | 2725 | 2743 | a | C | A | G | A | C | A | C | A | U | g | C | U | C | C | U | C | c | c | 29 | 4 | 9 | c | false | <90% | 4034 | ||
| XM_942428 | DUSP27 | 2725 | 2743 | a | C | A | G | A | C | A | C | A | U | g | C | U | C | C | U | C | c | c | 29 | 4 | 9 | c | false | <90% | 4034 | ||
| NM_002062 | GLP1R | 2963 | 2981 | C | C | A | G | A | C | A | C | A | U | u | C | U | C | C | U | g | u | G | 12 | 3 | 10 | c | false | <90% | 3071 | ||
| NM_003399 | XPNPEP2 | 1274 | 1292 | a | C | A | G | A | C | A | C | c | U | A | C | U | C | C | c | C | A | G | 11 | 3 | 7 | c | false | <90% | 3333 | ||
| NM_012198 | GCA | 239 | 257 | u | C | A | G | A | C | A | C | u | U | A | u | U | C | C | U | C | A | G | 4 | 3 | 7 | false | <90% | 1642 | |||
| NM_052867 | NALCN | 862 | 880 | C | C | A | G | A | C | A | C | A | c | A | C | U | g | C | U | C | A | c | -7 | 3 | 9 | c | false | <90% | 6923 | ||
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_152475 | ZNF417 | 4316 | 4334 | C | U | G | A | a | G | A | G | U | A | U | G | U | G | U | C | U | G | u | 43 | 2 | 13 | bc | false | <90% | 4703 | ||
| NM_005358 | LMO7 | 6063 | 6081 | C | U | u | A | G | G | u | G | U | A | U | G | U | G | U | C | U | G | a | 9 | 3 | 11 | bc | false | <90% | 7235 | ||
| NM_024322 | CENPO | 488 | 506 | C | c | G | A | G | G | A | G | U | u | U | G | U | G | U | C | U | G | c | 0 | 3 | 8 | bc | false | <90% | 1665 | ||
| NM_014838 | ZBED4 | 1106 | 1124 | C | a | G | A | G | G | A | G | U | c | U | G | U | G | U | C | U | G | u | 0 | 3 | 8 | bc | false | <90% | 5217 | ||
| NR_003208 | SNORD114-15 | 41 | 59 | a | U | G | A | u | G | A | a | U | A | U | G | U | G | U | C | U | G | G | -15 | 3 | 11 | bc | false | <90% | 71 | ||
| NM_023007 | JMJD4 | 1694 | 1712 | g | a | c | A | G | G | A | G | U | c | U | G | U | G | U | C | U | G | G | -15 | 4 | 9 | bc | false | <90% | 2550 | ||
| NM_014423 | AFF4 | 7750 | 7768 | u | a | u | A | G | G | A | G | U | u | U | G | U | G | U | C | U | G | G | -15 | 4 | 9 | bc | false | <90% | 9580 | ||
3 prime UTR Seed matches
Hits to same gene : 0
Hits to other genes : 2167
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)
Motif found in sense strand
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