Automatic recommendation
OK - siRNA is specific for both sense and antisense (guide) strands
13 hits were found for UACACCCAAAGACCACAUU (4 guide strand hits and 9 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_138381 | OXNAD1 | 1357 | 1375 | U | g | u | A | C | C | C | A | A | A | G | A | a | C | A | C | A | U | U | 58 | 3 | 9 | false | <90% | 3945 | |||
| NM_004183 | BEST1 | 1799 | 1817 | U | A | C | A | C | u | C | A | A | A | G | A | u | C | A | C | A | U | g | 21 | 3 | 6 | false | <90% | 2673 | |||
| NM_001017924 | LRRC22 | 2090 | 2108 | U | A | C | A | C | C | C | A | g | A | G | u | C | C | A | C | A | U | c | 1 | 3 | 8 | false | <90% | 3096 | |||
| NM_020366 | RPGRIP1 | 1532 | 1550 | c | A | C | A | C | g | C | A | g | A | G | A | C | C | A | C | A | U | U | -25 | 3 | 10 | bc | false | <90% | 3950 | ||
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_015028 | TNIK | 647 | 665 | c | u | U | G | U | G | G | U | C | U | U | U | G | G | G | U | a | U | c | 58 | 4 | 14 | ac | false | <90% | 4083 | ||
| XR_019444 | LOC122589 | 251 | 269 | A | A | U | G | U | G | G | U | C | U | U | U | G | c | G | U | u | c | A | 54 | 3 | 13 | c | false | <90% | 1025 | ||
| NR_001444 | LYPLA2P1 | 1558 | 1576 | c | A | U | G | U | G | G | U | u | U | U | U | G | G | G | U | G | U | u | 32 | 3 | 9 | bc | false | <90% | 1639 | ||
| NM_007260 | LYPLA2 | 1556 | 1574 | c | A | U | G | U | G | G | U | u | U | U | U | G | G | G | U | G | U | u | 32 | 3 | 9 | bc | false | <90% | 1648 | ||
| XR_017654 | LOC388499 | 1512 | 1530 | c | A | U | G | U | G | G | U | u | U | U | U | G | G | G | U | G | c | u | 30 | 4 | 8 | c | false | <90% | 1596 | ||
| XM_001133411 | LOC388499 | 1511 | 1529 | c | A | U | G | U | G | G | U | u | U | U | U | G | G | G | U | G | c | u | 30 | 4 | 8 | c | false | <90% | 1600 | ||
| NM_000267 | NF1 | 7018 | 7036 | c | u | U | G | U | u | G | U | C | U | U | U | G | G | G | U | G | U | A | 23 | 3 | 13 | bc | false | <90% | 12331 | ||
| NM_001042492 | NF1 | 7081 | 7099 | c | u | U | G | U | u | G | U | C | U | U | U | G | G | G | U | G | U | A | 23 | 3 | 13 | bc | false | <90% | 12394 | ||
| NM_024577 | SH3TC2 | 26493 | 26511 | A | A | U | G | U | u | G | U | C | U | U | U | G | a | G | U | G | U | u | 12 | 3 | 7 | c | false | <90% | 26588 | ||
3 prime UTR Seed matches
Hits to same gene : 0
Hits to other genes : 845
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