Automatic recommendation
Warning - siRNA is specific for only the antisense (guide) strand
13 hits were found for AUCAACACCAUAAAGUACC (2 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_144773 | PROKR2 | 1012 | 1030 | A | a | C | A | A | C | A | C | C | A | U | g | A | A | G | U | A | C | u | 49 | 3 | 9 | false | <90% | 1155 | |||
| NM_020761 | KIAA1303 | 4664 | 4682 | A | U | C | A | A | C | A | a | C | A | U | c | A | A | G | U | A | C | u | 0 | 3 | 7 | false | <90% | 6856 | |||
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_001128 | AP1G1 | 3973 | 3991 | u | G | U | A | C | U | U | U | A | U | G | G | U | G | U | U | G | g | a | 90 | 3 | 16 | ac | false | <90% | 6841 | ||
| NM_001030007 | AP1G1 | 3982 | 4000 | u | G | U | A | C | U | U | U | A | U | G | G | U | G | U | U | G | g | a | 90 | 3 | 16 | ac | false | <90% | 6850 | ||
| NM_181558 | RFC3 | 281 | 299 | u | G | a | A | C | U | U | U | A | U | G | G | U | G | U | U | G | g | a | 70 | 4 | 14 | c | false | <90% | 1463 | ||
| NM_002915 | RFC3 | 281 | 299 | u | G | a | A | C | U | U | U | A | U | G | G | U | G | U | U | G | g | a | 70 | 4 | 14 | c | false | <90% | 2396 | ||
| NM_153705 | KDELC2 | 371 | 389 | G | G | U | c | C | U | U | U | A | U | G | G | U | G | a | U | G | A | a | 33 | 3 | 10 | c | false | <90% | 4264 | ||
| NM_012219 | MRAS | 133 | 151 | G | G | a | A | u | U | U | U | A | U | G | G | U | G | U | U | G | A | a | 23 | 3 | 13 | bc | false | <90% | 4454 | ||
| NM_001981 | EPS15 | 4836 | 4854 | G | G | U | A | u | U | U | U | A | U | G | u | U | G | U | U | G | A | c | 9 | 3 | 6 | false | <90% | 5220 | |||
| NM_001033025 | EXTL2 | 923 | 941 | a | G | U | A | C | U | c | U | A | U | G | G | U | G | c | U | G | A | U | 6 | 3 | 7 | c | false | <90% | 2869 | ||
| NM_001439 | EXTL2 | 959 | 977 | a | G | U | A | C | U | c | U | A | U | G | G | U | G | c | U | G | A | U | 6 | 3 | 7 | c | false | <90% | 2905 | ||
| NM_001186 | BACH1 | 3729 | 3747 | a | G | U | A | g | U | U | U | A | U | a | G | U | G | U | U | G | A | U | -14 | 3 | 8 | c | false | <90% | 5642 | ||
| NM_206866 | BACH1 | 3857 | 3875 | a | G | U | A | g | U | U | U | A | U | a | G | U | G | U | U | G | A | U | -14 | 3 | 8 | c | false | <90% | 5770 | ||
3 prime UTR Seed matches
Hits to same gene : 0
Hits to other genes : 1468
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