Automatic recommendation
OK - siRNA is specific for both sense and antisense (guide) strands
16 hits were found for GAGUGAGACGAGAAAUGCA (10 guide strand hits and 6 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_145251 | STYX | 332 | 350 | c | u | a | U | G | A | G | A | C | G | A | G | A | g | A | U | G | C | A | 47 | 4 | 10 | c | false | <90% | 2607 | ||
| XM_001125680 | LOC730432 | 125 | 143 | c | u | a | U | G | A | G | A | C | G | A | G | A | g | A | U | G | C | A | 47 | 4 | 10 | c | false | <90% | 4612 | ||
| XM_001125705 | LOC730432 | 388 | 406 | c | u | a | U | G | A | G | A | C | G | A | G | A | g | A | U | G | C | A | 47 | 4 | 10 | c | false | <90% | 4875 | ||
| NM_145246 | C10orf4 | 792 | 810 | u | g | G | U | G | A | G | A | a | G | A | G | A | A | A | U | G | C | A | 26 | 3 | 10 | bc | false | <90% | 2400 | ||
| NR_003262 | FDPSL2A | 2597 | 2615 | c | A | G | U | G | A | G | c | C | G | A | G | A | A | c | U | G | C | A | 11 | 3 | 6 | c | false | <90% | 4981 | ||
| NM_152524 | SGOL2 | 785 | 803 | G | A | G | U | G | A | G | A | u | G | A | G | A | A | A | c | G | C | c | 8 | 3 | 8 | c | false | <90% | 4214 | ||
| NM_004417 | DUSP1 | 1401 | 1419 | c | c | u | U | G | A | G | A | g | G | A | G | A | A | A | U | G | C | A | 6 | 4 | 10 | bc | false | <90% | 2015 | ||
| NM_003151 | STAT4 | 128 | 146 | a | A | G | U | G | g | G | A | g | G | A | G | A | A | A | U | G | C | A | -25 | 3 | 10 | bc | false | <90% | 2761 | ||
| NM_006134 | TMEM50B | 232 | 250 | G | A | G | U | G | A | G | A | g | a | A | G | A | A | A | U | G | C | u | -47 | 3 | 8 | bc | false | <90% | 2350 | ||
| NM_003787 | NOL4 | 1797 | 1815 | G | A | G | U | G | A | G | A | g | u | A | G | A | A | A | U | G | C | c | -47 | 3 | 8 | bc | false | <90% | 2619 | ||
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_015983 | UBE2D4 | 1119 | 1137 | g | G | C | A | U | U | U | C | U | C | G | c | C | U | C | A | C | a | C | 61 | 3 | 10 | false | <90% | 1398 | |||
| NM_152735 | ZBTB9 | 1871 | 1889 | c | a | a | A | U | U | U | C | U | C | G | U | C | c | C | A | C | U | C | 47 | 4 | 10 | c | false | <90% | 2730 | ||
| NM_138473 | SP1 | 2748 | 2766 | U | G | C | A | U | U | U | C | U | C | u | U | C | U | C | A | g | c | u | 7 | 4 | 10 | c | false | <90% | 7667 | ||
| NM_005070 | SLC4A3 | 2493 | 2511 | U | G | C | c | U | U | U | C | U | C | a | U | C | U | C | A | C | U | C | 1 | 2 | 8 | c | false | <90% | 3943 | ||
| NM_201574 | SLC4A3 | 2782 | 2800 | U | G | C | c | U | U | U | C | U | C | a | U | C | U | C | A | C | U | C | 1 | 2 | 8 | c | false | <90% | 4257 | ||
| NM_019116 | UBFD1 | 2486 | 2504 | U | G | C | A | g | U | U | C | U | C | c | U | C | U | C | A | C | U | g | -17 | 3 | 7 | c | false | <90% | 4931 | ||
3 prime UTR Seed matches
Hits to same gene : 0
Hits to other genes : 2486
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