Automatic recommendation
OK - siRNA is specific for both sense and antisense (guide) strands
11 hits were found for CCAUACUGCGGAACUCCUA (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_012161 | FBXL5 | 589 | 607 | g | g | A | U | A | C | U | G | C | a | G | A | A | C | U | C | C | U | u | -1 | 4 | 8 | bc | false | <90% | 3371 | ||
| NM_033535 | FBXL5 | 693 | 711 | g | g | A | U | A | C | U | G | C | a | G | A | A | C | U | C | C | U | u | -1 | 4 | 8 | bc | false | <90% | 3475 | ||
| NM_138473 | SP1 | 3749 | 3767 | C | C | A | U | u | C | U | G | C | a | G | A | A | C | U | C | C | U | c | -39 | 3 | 8 | bc | false | <90% | 7667 | ||
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_003793 | CTSF | 814 | 832 | g | A | G | G | A | G | U | U | C | C | G | C | A | c | U | A | U | c | u | 70 | 4 | 12 | c | false | <90% | 2032 | ||
| NM_015512 | DNAH1 | 2609 | 2627 | g | A | G | G | A | G | U | U | C | C | G | C | A | G | c | A | U | c | a | 65 | 4 | 13 | c | false | <90% | 13114 | ||
| NM_198525 | KIF7 | 998 | 1016 | c | A | G | G | A | G | U | U | C | C | G | C | A | G | g | A | g | G | G | 49 | 3 | 13 | c | false | <90% | 3121 | ||
| NM_015001 | SPEN | 1624 | 1642 | a | u | G | G | A | G | U | U | C | C | u | C | A | G | U | A | U | G | c | 20 | 4 | 8 | c | false | <90% | 12227 | ||
| NM_145234 | CHRDL1 | 1848 | 1866 | U | A | G | G | A | G | U | U | C | u | G | C | A | G | U | A | U | a | G | 14 | 2 | 9 | c | false | <90% | 2488 | ||
| NR_003228 | AFG3L1 | 539 | 557 | g | A | G | G | A | u | U | U | C | C | G | C | A | G | U | c | U | G | G | 8 | 3 | 9 | c | false | <90% | 1941 | ||
| NR_003227 | AFG3L1 | 500 | 518 | g | A | G | G | A | u | U | U | C | C | G | C | A | G | U | c | U | G | G | 8 | 3 | 9 | c | false | <90% | 2947 | ||
| NR_003226 | AFG3L1 | 573 | 591 | g | A | G | G | A | u | U | U | C | C | G | C | A | G | U | c | U | G | G | 8 | 3 | 9 | c | false | <90% | 3186 | ||
3 prime UTR Seed matches
Hits to same gene : 0
Hits to other genes : 1218
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