Automatic recommendation
Not OK - siRNA is not specific
16 hits were found for GAAAGGAGUUGGAACAAUA (12 guide strand hits and 4 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_014635 | GCC2 | 360 | 378 | a | u | A | A | G | G | A | G | U | U | G | G | A | A | C | A | A | U | c | 81 | 3 | 16 | abc | false | <90% | 6833 | ||
| NM_181453 | GCC2 | 445 | 463 | a | u | A | A | G | G | A | G | U | U | G | G | A | A | C | A | A | U | c | 81 | 3 | 16 | abc | false | <90% | 6918 | ||
| NM_021619 | PRDM12 | 1947 | 1965 | u | g | A | A | G | G | A | G | U | U | G | G | A | c | C | A | A | U | g | 62 | 4 | 11 | c | false | <90% | 2492 | ||
| NM_022458 | LMBR1 | 1000 | 1018 | u | A | A | u | G | G | A | G | U | U | G | G | A | A | C | A | A | g | A | 58 | 3 | 13 | c | false | <90% | 4909 | ||
| NM_020711 | KIAA1189 | 153 | 171 | a | g | u | A | G | G | A | G | U | U | G | G | A | A | C | u | A | U | A | 40 | 4 | 12 | c | false | <90% | 3790 | ||
| NM_139179 | DAGLB | 2805 | 2823 | u | u | c | A | G | G | A | G | U | U | G | a | A | A | C | A | A | U | A | 33 | 4 | 8 | false | <90% | 2863 | |||
| NM_014915 | ANKRD26 | 4499 | 4517 | a | A | A | A | G | a | A | G | U | U | G | G | A | A | C | A | A | g | A | 32 | 3 | 11 | c | false | <90% | 5360 | ||
| NM_032374 | C14orf153 | 540 | 558 | G | A | A | A | G | G | A | u | U | U | G | G | A | A | C | A | A | g | c | 30 | 3 | 9 | c | false | <90% | 2497 | ||
| NM_007118 | TRIO | 4073 | 4091 | u | A | A | A | G | G | A | G | c | U | G | G | A | A | a | A | A | U | A | 13 | 3 | 7 | c | false | <90% | 10244 | ||
| NM_025134 | CHD9 | 7678 | 7696 | G | A | A | A | G | G | A | u | U | U | G | G | A | A | a | A | A | U | g | 8 | 3 | 7 | c | false | <90% | 11479 | ||
| NM_001002758 | PRY2 | 1194 | 1212 | u | A | A | A | G | u | A | G | U | U | G | a | A | A | C | A | A | U | A | 0 | 3 | 7 | false | <90% | 1238 | |||
| NM_004676 | PRY | 1194 | 1212 | u | A | A | A | G | u | A | G | U | U | G | a | A | A | C | A | A | U | A | 0 | 3 | 7 | false | <90% | 1238 | |||
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_153607 | LOC153222 | 2932 | 2950 | U | u | U | U | G | U | U | C | C | A | A | C | U | C | u | U | U | U | u | 58 | 3 | 12 | c | false | <90% | 5446 | ||
| NM_016529 | ATP8A2 | 1876 | 1894 | a | A | U | U | G | U | U | C | g | A | A | C | U | C | C | U | U | c | a | 30 | 4 | 8 | c | false | <90% | 5006 | ||
| NM_024106 | ZNF426 | 1218 | 1236 | a | A | U | U | a | U | U | C | C | A | A | C | U | C | a | U | U | U | C | 21 | 3 | 9 | c | false | <90% | 2320 | ||
| NM_152262 | ZNF439 | 1739 | 1757 | a | A | U | U | G | U | U | C | C | A | g | u | U | C | C | U | U | U | C | 2 | 3 | 9 | false | <90% | 2566 | |||
3 prime UTR Seed matches
Hits to same gene : 0
Hits to other genes : 3309
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