Automatic recommendation
OK - siRNA is specific for both sense and antisense (guide) strands
19 hits were found for GGAAAGGACAUGUCUCUAU (17 guide strand hits and 2 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_014227 | SLC5A4 | 926 | 944 | G | G | c | A | A | G | G | A | C | A | U | G | U | C | U | C | a | c | g | 49 | 4 | 13 | c | false | <90% | 2043 | ||
| XM_001126138 | LOC727851 | 1049 | 1067 | u | G | A | A | A | G | G | A | C | A | U | u | U | C | U | a | U | A | U | 38 | 3 | 10 | false | <90% | 2961 | |||
| XM_001133575 | LOC729540 | 1390 | 1408 | u | G | A | A | A | G | G | A | C | A | U | u | U | C | U | a | U | A | U | 38 | 3 | 10 | false | <90% | 3304 | |||
| NM_001037866 | RGPD7 | 1390 | 1408 | u | G | A | A | A | G | G | A | C | A | U | u | U | C | U | a | U | A | U | 38 | 3 | 10 | false | <90% | 3304 | |||
| NM_032260 | RGPD5 | 1390 | 1408 | u | G | A | A | A | G | G | A | C | A | U | u | U | C | U | a | U | A | U | 38 | 3 | 10 | false | <90% | 3325 | |||
| XM_001133578 | LOC729540 | 1864 | 1882 | u | G | A | A | A | G | G | A | C | A | U | u | U | C | U | a | U | A | U | 38 | 3 | 10 | false | <90% | 3776 | |||
| XM_001126152 | LOC727851 | 1049 | 1067 | u | G | A | A | A | G | G | A | C | A | U | u | U | C | U | a | U | A | U | 38 | 3 | 10 | false | <90% | 5708 | |||
| XM_001133583 | LOC729540 | 1864 | 1882 | u | G | A | A | A | G | G | A | C | A | U | u | U | C | U | a | U | A | U | 38 | 3 | 10 | false | <90% | 6523 | |||
| XM_001133581 | LOC729540 | 1864 | 1882 | u | G | A | A | A | G | G | A | C | A | U | u | U | C | U | a | U | A | U | 38 | 3 | 10 | false | <90% | 6593 | |||
| XM_001126221 | LOC727851 | 177 | 195 | u | G | A | A | A | G | G | A | C | A | U | u | U | C | U | a | U | A | U | 38 | 3 | 10 | false | <90% | 6620 | |||
| NM_005054 | RGPD5 | 934 | 952 | u | G | A | A | A | G | G | A | C | A | U | u | U | C | U | a | U | A | U | 38 | 3 | 10 | false | <90% | 7182 | |||
| XM_001126248 | LOC727851 | 954 | 972 | u | G | A | A | A | G | G | A | C | A | U | u | U | C | U | a | U | A | U | 38 | 3 | 10 | false | <90% | 7397 | |||
| XM_001126272 | LOC727851 | 1049 | 1067 | u | G | A | A | A | G | G | A | C | A | U | u | U | C | U | a | U | A | U | 38 | 3 | 10 | false | <90% | 7507 | |||
| XM_001133590 | LOC729540 | 1177 | 1195 | u | G | A | A | A | G | G | A | C | A | U | u | U | C | U | a | U | A | U | 38 | 3 | 10 | false | <90% | 7620 | |||
| XM_001133591 | LOC729540 | 1864 | 1882 | u | G | A | A | A | G | G | A | C | A | U | u | U | C | U | a | U | A | U | 38 | 3 | 10 | false | <90% | 8322 | |||
| NM_014515 | CNOT2 | 563 | 581 | G | G | A | A | A | G | G | A | C | A | c | G | a | C | U | C | U | A | U | 28 | 2 | 10 | false | <90% | 3280 | |||
| NM_080797 | DIDO1 | 5607 | 5625 | G | G | A | A | A | G | G | A | C | A | g | G | U | C | U | C | c | c | a | 7 | 4 | 10 | c | false | <90% | 7610 | ||
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_013443 | ST6GALNAC6 | 1408 | 1426 | c | U | A | a | g | G | A | C | A | U | G | U | C | C | U | U | U | C | C | 9 | 3 | 14 | bc | false | <90% | 2416 | ||
| NM_019084 | CCNJ | 3137 | 3155 | u | U | A | G | A | G | A | a | A | U | a | U | C | C | U | U | U | C | C | -25 | 3 | 8 | c | false | <90% | 4123 | ||
3 prime UTR Seed matches
Hits to same gene : 0
Hits to other genes : 3316
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