Automatic recommendation
OK - siRNA is specific for both sense and antisense (guide) strands
19 hits were found for CCAUGACACCAGCUGAUAA (11 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_004797 | ADIPOQ | 804 | 822 | C | C | A | U | G | A | C | A | C | C | A | a | C | U | G | A | U | c | A | 63 | 2 | 11 | false | <90% | 4592 | |||
| NM_052909 | KIAA1909 | 10215 | 10233 | C | C | A | U | G | A | C | A | C | C | A | G | C | U | G | g | g | u | g | 42 | 4 | 15 | c | false | <90% | 11507 | ||
| NM_001010854 | TTC7B | 3128 | 3146 | C | C | A | g | G | A | C | A | C | C | A | G | C | U | G | A | c | A | A | 39 | 2 | 12 | c | false | <90% | 3443 | ||
| NM_000595 | LTA | 139 | 157 | C | C | A | U | G | A | C | A | C | C | A | c | C | U | G | A | a | c | g | 35 | 4 | 11 | false | <90% | 1386 | |||
| NM_182503 | DEADC1 | 2918 | 2936 | C | C | A | a | G | A | C | A | C | C | A | G | C | U | G | A | a | A | g | 34 | 3 | 12 | c | false | <90% | 6270 | ||
| NM_134259 | TBL1Y | 920 | 938 | C | C | A | U | G | A | C | c | C | C | A | G | C | U | G | c | U | A | u | 6 | 3 | 7 | c | false | <90% | 2312 | ||
| NM_134258 | TBL1Y | 984 | 1002 | C | C | A | U | G | A | C | c | C | C | A | G | C | U | G | c | U | A | u | 6 | 3 | 7 | c | false | <90% | 2376 | ||
| NM_033284 | TBL1Y | 1015 | 1033 | C | C | A | U | G | A | C | c | C | C | A | G | C | U | G | c | U | A | u | 6 | 3 | 7 | c | false | <90% | 2407 | ||
| NM_052900 | CSMD3 | 6429 | 6447 | C | C | A | U | G | A | a | A | C | C | A | G | C | U | u | A | U | A | u | 4 | 3 | 7 | c | false | <90% | 12643 | ||
| NM_198124 | CSMD3 | 6633 | 6651 | C | C | A | U | G | A | a | A | C | C | A | G | C | U | u | A | U | A | u | 4 | 3 | 7 | c | false | <90% | 13042 | ||
| NM_198123 | CSMD3 | 6741 | 6759 | C | C | A | U | G | A | a | A | C | C | A | G | C | U | u | A | U | A | u | 4 | 3 | 7 | c | false | <90% | 13150 | ||
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_144701 | IL23R | 139 | 157 | U | c | u | U | C | A | G | C | U | G | G | U | G | U | C | A | U | G | G | 69 | 2 | 16 | bc | false | <90% | 2826 | ||
| NM_001010980 | C1orf130 | 3796 | 3814 | U | U | A | g | C | A | G | C | U | G | G | U | c | U | C | A | U | G | c | 47 | 3 | 8 | false | <90% | 3953 | |||
| NM_004513 | IL16 | 2639 | 2657 | g | c | A | U | C | A | G | C | U | G | G | c | G | U | C | A | U | G | c | 47 | 4 | 9 | false | <90% | 6193 | |||
| NM_172217 | IL16 | 5061 | 5079 | g | c | A | U | C | A | G | C | U | G | G | c | G | U | C | A | U | G | c | 47 | 4 | 9 | false | <90% | 8615 | |||
| NM_021159 | RAP1GDS1 | 1293 | 1311 | U | U | A | U | C | A | G | C | U | G | G | g | G | U | C | A | c | a | G | 40 | 3 | 11 | false | <90% | 2487 | |||
| XM_497341 | MUC19 | 16752 | 16770 | c | U | A | U | C | A | G | C | U | G | G | a | G | U | g | A | U | G | G | 39 | 3 | 10 | false | <90% | 21987 | |||
| NM_001040272 | C9orf94 | 484 | 502 | a | U | A | U | C | A | c | C | U | G | G | U | u | U | C | A | U | G | G | 21 | 3 | 6 | false | <90% | 1876 | |||
| NM_014905 | GLS | 797 | 815 | a | c | A | U | C | A | G | a | U | G | G | U | G | U | C | A | U | G | c | 19 | 4 | 10 | bc | false | <90% | 4799 | ||
3 prime UTR Seed matches
Hits to same gene : 0
Hits to other genes : 1358
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