Automatic recommendation
Not OK - siRNA is not specific
11 hits were found for UGUGUACUGCAAGCAACAG (9 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_032578 | MYPN | 2028 | 2046 | c | a | U | G | U | A | C | U | G | C | A | A | G | C | A | A | C | A | a | 81 | 3 | 16 | abc | false | <90% | 5707 | ||
| NR_002771 | DLEU2L | 348 | 366 | g | G | U | G | U | A | C | U | G | C | A | A | G | g | A | A | C | A | a | 73 | 3 | 12 | c | false | <90% | 1657 | ||
| NR_002612 | DLEU2 | 435 | 453 | g | G | U | G | U | A | C | U | G | C | A | A | G | g | A | A | C | A | a | 73 | 3 | 12 | c | false | <90% | 2768 | ||
| NM_005120 | MED12 | 4401 | 4419 | g | a | a | G | U | A | C | U | G | C | A | A | G | C | A | A | C | A | u | 62 | 4 | 15 | bc | false | <90% | 6985 | ||
| NM_182607 | VSIG1 | 790 | 808 | a | G | U | G | U | A | C | U | G | C | c | A | u | C | A | A | C | A | G | 26 | 3 | 9 | false | <90% | 3145 | |||
| NM_014989 | RIMS1 | 2361 | 2379 | a | a | U | G | U | u | C | U | G | C | A | A | G | C | A | A | C | A | G | 23 | 3 | 13 | bc | false | <90% | 7248 | ||
| NM_002157 | HSPE1 | 159 | 177 | a | a | a | G | U | A | u | U | G | C | A | A | G | C | A | A | C | A | G | 0 | 4 | 12 | bc | false | <90% | 538 | ||
| NM_002432 | MNDA | 843 | 861 | g | u | g | G | U | A | C | U | G | a | A | A | G | C | A | A | C | A | G | -15 | 4 | 9 | bc | false | <90% | 1670 | ||
| NM_133493 | CD109 | 1448 | 1466 | U | G | U | G | U | u | C | U | u | C | A | A | G | C | A | A | C | A | u | -28 | 3 | 9 | bc | false | <90% | 9447 | ||
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_005077 | TLE1 | 3092 | 3110 | C | U | G | U | U | c | C | U | U | G | C | A | G | U | u | C | A | C | c | 7 | 3 | 8 | c | false | <90% | 3283 | ||
| NM_015190 | DNAJC9 | 526 | 544 | g | c | u | U | U | G | C | g | U | G | C | A | G | U | A | C | A | C | A | 4 | 4 | 11 | bc | false | <90% | 1450 | ||
3 prime UTR Seed matches
Hits to same gene : 0
Hits to other genes : 2230
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 guide 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