Automatic recommendation
OK - siRNA is specific for both sense and antisense (guide) strands
23 hits were found for GGGAUAACACCAGCAAUAU (15 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_147175 | HS6ST2 | 2176 | 2194 | a | u | G | A | U | A | A | C | A | C | C | A | G | C | A | A | U | g | g | 78 | 4 | 15 | ac | false | <90% | 4456 | ||
| NM_001077188 | HS6ST2 | 2296 | 2314 | a | u | G | A | U | A | A | C | A | C | C | A | G | C | A | A | U | g | g | 78 | 4 | 15 | ac | false | <90% | 4576 | ||
| NM_182749 | N6AMT1 | 2877 | 2895 | G | u | a | A | U | A | A | C | A | C | C | A | G | C | u | A | U | A | U | 44 | 3 | 11 | c | false | <90% | 4799 | ||
| NM_013240 | N6AMT1 | 2961 | 2979 | G | u | a | A | U | A | A | C | A | C | C | A | G | C | u | A | U | A | U | 44 | 3 | 11 | c | false | <90% | 4883 | ||
| NM_001429 | EP300 | 4991 | 5009 | a | G | G | A | a | A | A | C | A | C | C | A | G | C | A | A | U | g | a | 38 | 4 | 12 | c | false | <90% | 8765 | ||
| NM_181719 | TMCO4 | 2913 | 2931 | G | G | G | A | U | A | A | C | A | a | C | A | G | C | A | A | U | A | a | 12 | 2 | 9 | bc | false | <90% | 2964 | ||
| XM_943442 | LOC440597 | 473 | 491 | G | G | G | A | U | A | A | u | A | C | C | u | G | C | A | A | U | A | U | 4 | 2 | 7 | false | <90% | 527 | |||
| XM_498747 | LOC440597 | 473 | 491 | G | G | G | A | U | A | A | u | A | C | C | u | G | C | A | A | U | A | U | 4 | 2 | 7 | false | <90% | 527 | |||
| NM_024947 | PHC3 | 1456 | 1474 | u | c | c | A | U | c | A | C | A | C | C | A | G | C | A | A | U | A | U | 3 | 4 | 13 | bc | false | <90% | 3319 | ||
| XR_019281 | LOC651924 | 50 | 68 | G | G | G | A | U | A | u | C | A | C | C | A | G | C | A | A | g | g | a | 2 | 4 | 9 | c | false | <90% | 1136 | ||
| XR_016894 | LOC645503 | 50 | 68 | G | G | G | A | U | A | u | C | A | C | C | A | G | C | A | A | g | g | a | 2 | 4 | 9 | c | false | <90% | 1136 | ||
| NM_001079669 | TMTC4 | 2531 | 2549 | a | u | u | A | U | A | g | C | A | C | C | A | G | C | A | A | U | A | U | 0 | 4 | 12 | bc | false | <90% | 3561 | ||
| NM_032813 | TMTC4 | 2741 | 2759 | a | u | u | A | U | A | g | C | A | C | C | A | G | C | A | A | U | A | U | 0 | 4 | 12 | bc | false | <90% | 3771 | ||
| XM_937409 | ZNF516 | 2735 | 2753 | G | G | G | A | U | g | A | C | c | C | C | A | G | C | A | A | U | A | a | -28 | 3 | 9 | bc | false | <90% | 8815 | ||
| XM_496278 | ZNF516 | 2735 | 2753 | G | G | G | A | U | g | A | C | c | C | C | A | G | C | A | A | U | A | a | -28 | 3 | 9 | bc | false | <90% | 8822 | ||
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 | |||||||||||||
| XM_937019 | C9orf57 | 308 | 326 | u | U | u | U | U | G | C | U | G | G | U | G | U | U | A | U | C | u | u | 70 | 4 | 14 | c | false | <90% | 1629 | ||
| XM_059954 | C9orf57 | 308 | 326 | u | U | u | U | U | G | C | U | G | G | U | G | U | U | A | U | C | u | u | 70 | 4 | 14 | c | false | <90% | 1629 | ||
| NM_003193 | TBCE | 196 | 214 | g | U | u | U | U | G | C | U | G | G | U | G | U | U | g | U | C | C | C | 53 | 3 | 11 | c | false | <90% | 1925 | ||
| NM_001079515 | TBCE | 244 | 262 | g | U | u | U | U | G | C | U | G | G | U | G | U | U | g | U | C | C | C | 53 | 3 | 11 | c | false | <90% | 1973 | ||
| NM_006895 | HNMT | 1305 | 1323 | A | U | A | c | U | G | C | U | G | G | U | c | U | U | A | U | C | C | u | 24 | 3 | 7 | false | <90% | 3373 | |||
| NM_052859 | RFT1 | 1289 | 1307 | u | c | A | U | U | c | C | U | G | G | U | G | U | U | A | U | C | C | u | 18 | 4 | 12 | bc | false | <90% | 2810 | ||
| XM_942001 | LOC652522 | 2967 | 2985 | u | U | A | U | U | G | C | U | G | a | U | G | U | U | A | U | C | C | g | 10 | 3 | 8 | bc | false | <90% | 3321 | ||
| NM_000553 | WRN | 4733 | 4751 | u | U | A | U | U | G | C | U | G | a | U | G | U | U | A | U | C | C | g | 10 | 3 | 8 | bc | false | <90% | 5745 | ||
3 prime UTR Seed matches
Hits to same gene : 0
Hits to other genes : 1178
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