Automatic recommendation
Warning - siRNA is specific for only the antisense (guide) strand
24 hits were found for CGAUAAUAUAACUGCAAGA (10 guide strand hits and 14 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_002025 | AFF2 | 11545 | 11563 | u | G | A | U | A | A | U | A | U | A | A | C | U | G | C | A | u | u | A | 71 | 3 | 15 | ac | false | <90% | 13746 | ||
| XM_927076 | LOC643797 | 1221 | 1239 | a | a | u | U | A | A | U | A | U | A | A | C | U | G | C | A | A | G | u | 62 | 4 | 15 | bc | false | <90% | 1568 | ||
| XM_938949 | LOC643797 | 1221 | 1239 | a | a | u | U | A | A | U | A | U | A | A | C | U | G | C | A | A | G | u | 62 | 4 | 15 | bc | false | <90% | 1568 | ||
| NM_000644 | AGL | 3840 | 3858 | u | u | u | U | A | A | U | A | U | A | A | C | U | G | C | A | g | G | A | 43 | 4 | 13 | c | false | <90% | 7109 | ||
| NM_000643 | AGL | 3900 | 3918 | u | u | u | U | A | A | U | A | U | A | A | C | U | G | C | A | g | G | A | 43 | 4 | 13 | c | false | <90% | 7169 | ||
| NM_000645 | AGL | 3913 | 3931 | u | u | u | U | A | A | U | A | U | A | A | C | U | G | C | A | g | G | A | 43 | 4 | 13 | c | false | <90% | 7182 | ||
| NM_000646 | AGL | 3913 | 3931 | u | u | u | U | A | A | U | A | U | A | A | C | U | G | C | A | g | G | A | 43 | 4 | 13 | c | false | <90% | 7182 | ||
| NM_000642 | AGL | 4102 | 4120 | u | u | u | U | A | A | U | A | U | A | A | C | U | G | C | A | g | G | A | 43 | 4 | 13 | c | false | <90% | 7371 | ||
| NM_000028 | AGL | 4180 | 4198 | u | u | u | U | A | A | U | A | U | A | A | C | U | G | C | A | g | G | A | 43 | 4 | 13 | c | false | <90% | 7449 | ||
| NM_153834 | GPR112 | 2982 | 3000 | g | G | A | U | A | A | U | A | a | A | A | C | U | G | C | A | A | c | A | 35 | 3 | 8 | c | false | <90% | 9931 | ||
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_021912 | GABRB3 | 2435 | 2453 | c | C | U | U | G | C | A | G | U | U | A | U | g | U | U | A | U | C | a | 82 | 3 | 11 | false | <90% | 5725 | |||
| NM_000814 | GABRB3 | 2521 | 2539 | c | C | U | U | G | C | A | G | U | U | A | U | g | U | U | A | U | C | a | 82 | 3 | 11 | false | <90% | 5811 | |||
| XM_370909 | LOC388177 | 914 | 932 | a | C | U | U | G | C | A | G | U | U | A | U | A | U | U | A | a | u | u | 66 | 4 | 15 | ac | false | <90% | 1037 | ||
| XM_938956 | LOC388177 | 1037 | 1055 | a | C | U | U | G | C | A | G | U | U | A | U | A | U | U | A | a | u | u | 66 | 4 | 15 | ac | false | <90% | 1160 | ||
| XM_001128623 | LOC728849 | 8107 | 8125 | U | C | U | U | G | C | A | G | U | U | A | U | c | U | U | A | g | C | a | 61 | 3 | 12 | false | <90% | 10120 | |||
| NM_138270 | ATRX | 8222 | 8240 | U | C | U | U | G | C | A | G | U | U | A | U | c | U | U | A | g | C | a | 61 | 3 | 12 | false | <90% | 11088 | |||
| NM_000489 | ATRX | 8336 | 8354 | U | C | U | U | G | C | A | G | U | U | A | U | c | U | U | A | g | C | a | 61 | 3 | 12 | false | <90% | 11202 | |||
| NM_001763 | CD1A | 922 | 940 | U | C | U | U | G | C | A | G | U | U | A | g | c | U | U | A | U | C | a | 50 | 3 | 11 | false | <90% | 2111 | |||
| NM_019042 | PUS7 | 2780 | 2798 | U | u | U | U | G | C | A | u | U | U | A | U | A | U | U | A | U | C | a | 21 | 3 | 10 | bc | false | <90% | 3484 | ||
| NM_017444 | CHRAC1 | 462 | 480 | U | C | U | U | G | C | A | G | a | U | A | U | A | U | U | A | c | C | a | 11 | 3 | 8 | c | false | <90% | 2496 | ||
| NM_006449 | CDC42EP3 | 3373 | 3391 | U | C | U | U | G | C | A | G | U | U | c | U | A | U | c | A | U | C | u | 9 | 3 | 10 | c | false | <90% | 3981 | ||
| XM_942521 | USP24 | 7790 | 7808 | U | C | U | U | G | C | A | G | U | a | A | U | A | U | U | A | a | a | c | -13 | 4 | 9 | c | false | <90% | 10051 | ||
| XM_371254 | USP24 | 7808 | 7826 | U | C | U | U | G | C | A | G | U | a | A | U | A | U | U | A | a | a | c | -13 | 4 | 9 | c | false | <90% | 10069 | ||
| NM_005084 | PLA2G7 | 455 | 473 | U | C | U | U | G | C | g | u | U | U | A | U | A | U | U | A | U | C | c | -33 | 3 | 10 | bc | false | <90% | 1561 | ||
3 prime UTR Seed matches
Hits to same gene : 0
Hits to other genes : 167
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