Automatic recommendation
Warning - siRNA is specific for only the antisense (guide) strand
25 hits were found for AGGAUUUAUUUAACAUAGA (14 guide strand hits and 11 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_000163 | GHR | 3301 | 3319 | A | G | G | A | U | U | U | A | U | U | U | A | A | a | A | U | A | G | c | 75 | 2 | 13 | c | false | <90% | 4370 | ||
| NM_001495 | GFRA2 | 662 | 680 | g | G | G | A | U | U | U | A | U | U | U | A | A | C | A | U | g | a | u | 66 | 4 | 15 | ac | false | <90% | 3376 | ||
| NM_032131 | ARMC2 | 694 | 712 | g | G | G | A | U | U | U | A | U | U | U | A | A | C | A | a | A | a | u | 64 | 4 | 14 | c | false | <90% | 3277 | ||
| XR_018481 | LOC648985 | 4064 | 4082 | g | u | u | A | U | U | U | A | U | U | U | A | g | C | A | U | A | G | A | 56 | 4 | 9 | false | <90% | 4238 | |||
| NM_014783 | ARHGAP11A | 4949 | 4967 | g | u | u | A | U | U | U | A | U | U | U | A | g | C | A | U | A | G | A | 56 | 4 | 9 | false | <90% | 5616 | |||
| NM_015192 | PLCB1 | 4188 | 4206 | c | u | a | A | U | U | U | A | U | U | U | A | u | C | A | U | A | G | A | 56 | 4 | 9 | false | <90% | 6705 | |||
| NM_182734 | PLCB1 | 4306 | 4324 | c | u | a | A | U | U | U | A | U | U | U | A | u | C | A | U | A | G | A | 56 | 4 | 9 | false | <90% | 6823 | |||
| XM_938891 | SMCHD1 | 6401 | 6419 | u | G | a | A | U | U | U | A | U | U | U | A | A | C | A | a | A | G | A | 52 | 3 | 12 | c | false | <90% | 8458 | ||
| XM_113962 | SMCHD1 | 6401 | 6419 | u | G | a | A | U | U | U | A | U | U | U | A | A | C | A | a | A | G | A | 52 | 3 | 12 | c | false | <90% | 8462 | ||
| NM_001077484 | SLC38A1 | 4481 | 4499 | A | a | u | A | U | U | U | A | U | U | U | A | A | a | A | U | A | G | A | 49 | 3 | 10 | c | false | <90% | 8148 | ||
| NM_030674 | SLC38A1 | 4820 | 4838 | A | a | u | A | U | U | U | A | U | U | U | A | A | a | A | U | A | G | A | 49 | 3 | 10 | c | false | <90% | 8487 | ||
| NM_006389 | HYOU1 | 3201 | 3219 | u | c | u | A | U | U | U | A | U | U | U | A | A | C | A | U | c | G | A | 43 | 4 | 13 | c | false | <90% | 4552 | ||
| NM_005638 | SYBL1 | 2212 | 2230 | u | u | c | A | U | U | U | A | U | U | U | g | A | C | A | U | A | G | A | 33 | 4 | 8 | false | <90% | 2588 | |||
| NM_004688 | NMI | 1098 | 1116 | A | G | G | A | U | U | U | A | a | U | U | A | A | C | A | U | u | c | A | 13 | 3 | 8 | c | false | <90% | 1426 | ||
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_015886 | PI15 | 5080 | 5098 | c | C | U | A | U | G | U | U | A | A | A | U | u | A | A | U | C | u | U | 84 | 3 | 11 | false | <90% | 6732 | |||
| NM_000627 | LTBP1 | 5101 | 5119 | U | g | U | A | U | G | U | U | A | A | A | U | A | A | A | U | C | a | c | 80 | 3 | 15 | ac | false | <90% | 5298 | ||
| NM_206943 | LTBP1 | 5951 | 5969 | U | g | U | A | U | G | U | U | A | A | A | U | A | A | A | U | C | a | c | 80 | 3 | 15 | ac | false | <90% | 6148 | ||
| NM_018993 | RIN2 | 3960 | 3978 | c | u | U | A | U | G | U | U | A | A | A | U | A | A | A | a | C | C | a | 55 | 4 | 13 | c | false | <90% | 4259 | ||
| NM_016053 | CCDC53 | 867 | 885 | U | C | U | A | U | G | U | U | A | A | A | a | A | A | A | U | a | a | U | 40 | 3 | 11 | false | <90% | 923 | |||
| NM_015144 | ZCCHC14 | 4860 | 4878 | a | a | U | A | U | u | U | U | A | A | A | U | A | A | A | U | C | C | U | 23 | 3 | 13 | bc | false | <90% | 6932 | ||
| NM_020337 | ANKRD50 | 7678 | 7696 | a | u | U | A | U | c | U | U | A | A | A | U | A | A | A | U | C | C | U | 23 | 3 | 13 | bc | false | <90% | 7763 | ||
| NM_006918 | SC5DL | 4769 | 4787 | U | a | U | A | U | G | U | U | u | A | A | U | A | A | A | U | C | C | c | 23 | 3 | 9 | bc | false | <90% | 6946 | ||
| NM_001024956 | SC5DL | 4842 | 4860 | U | a | U | A | U | G | U | U | u | A | A | U | A | A | A | U | C | C | c | 23 | 3 | 9 | bc | false | <90% | 7019 | ||
| NM_182830 | MDGA2 | 4695 | 4713 | g | C | U | A | U | G | U | U | c | A | A | U | A | A | A | g | C | C | U | 11 | 3 | 7 | c | false | <90% | 4747 | ||
| NM_033062 | KRTAP4-2 | 721 | 739 | U | C | U | A | U | c | U | U | A | A | A | U | A | A | A | U | u | u | U | 10 | 3 | 10 | c | false | <90% | 782 | ||
3 prime UTR Seed matches
Hits to same gene : 0
Hits to other genes : 3117
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