Automatic recommendation
Not OK - siRNA is not specific
21 hits were found for GCGAUGACAUGGAGAGAAA (15 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 | |||||||||||||
| XR_018463 | LOC644936 | 222 | 240 | G | g | G | A | U | G | A | C | A | U | G | G | A | G | A | G | A | g | A | 85 | 2 | 15 | ac | false | <90% | 1112 | ||
| XR_016742 | LOC644936 | 222 | 240 | G | g | G | A | U | G | A | C | A | U | G | G | A | G | A | G | A | g | A | 85 | 2 | 15 | ac | false | <90% | 1112 | ||
| XR_018464 | LOC139163 | 2617 | 2635 | G | u | G | A | U | G | A | C | A | U | G | G | A | G | A | G | c | u | A | 62 | 3 | 14 | ac | false | <90% | 3846 | ||
| XM_001131341 | STEAP1 | 217 | 235 | u | C | u | u | U | G | A | C | A | U | G | G | A | G | A | G | A | A | u | 36 | 4 | 14 | bc | false | <90% | 507 | ||
| XM_001128032 | MGC87042 | 770 | 788 | u | C | u | u | U | G | A | C | A | U | G | G | A | G | A | G | A | A | u | 36 | 4 | 14 | bc | false | <90% | 1192 | ||
| XM_001127055 | MGC87042 | 770 | 788 | u | C | u | u | U | G | A | C | A | U | G | G | A | G | A | G | A | A | u | 36 | 4 | 14 | bc | false | <90% | 1192 | ||
| XM_001128503 | MGC87042 | 770 | 788 | u | C | u | u | U | G | A | C | A | U | G | G | A | G | A | G | A | A | u | 36 | 4 | 14 | bc | false | <90% | 1192 | ||
| NM_012449 | STEAP1 | 930 | 948 | u | C | u | u | U | G | A | C | A | U | G | G | A | G | A | G | A | A | u | 36 | 4 | 14 | bc | false | <90% | 1330 | ||
| XM_001129065 | LOC729015 | 101 | 119 | c | g | G | A | g | G | A | C | A | U | G | G | A | G | A | G | A | A | A | 35 | 3 | 14 | bc | false | <90% | 1167 | ||
| XM_001129065 | LOC729015 | 695 | 713 | c | g | G | A | g | G | A | C | A | U | G | G | A | G | A | G | A | A | A | 35 | 3 | 14 | bc | false | <90% | 1167 | ||
| NM_006332 | IFI30 | 528 | 546 | u | u | G | A | g | G | A | C | A | U | G | G | A | G | A | G | A | A | g | 30 | 4 | 13 | bc | false | <90% | 1051 | ||
| NM_138381 | OXNAD1 | 600 | 618 | c | u | G | A | U | c | A | C | A | U | G | G | A | G | A | G | A | A | c | 18 | 4 | 12 | bc | false | <90% | 3945 | ||
| NM_004529 | MLLT3 | 1735 | 1753 | u | u | a | A | U | G | A | C | A | U | u | G | A | G | A | G | A | A | A | 5 | 4 | 8 | c | false | <90% | 3376 | ||
| NM_016571 | GLULD1 | 1219 | 1237 | c | a | a | A | U | G | u | C | A | U | G | G | A | G | A | G | A | A | A | 0 | 4 | 12 | bc | false | <90% | 1947 | ||
| NM_012424 | RPS6KC1 | 3028 | 3046 | G | C | G | A | U | G | c | C | A | U | a | G | A | G | A | G | A | A | u | -32 | 3 | 7 | c | false | <90% | 4196 | ||
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 | |||||||||||||
| XM_374124 | LOC389300 | 539 | 557 | a | U | U | C | U | C | U | C | C | A | U | G | U | C | A | c | C | G | C | 71 | 2 | 14 | c | false | <90% | 609 | ||
| XM_943175 | LOC389300 | 674 | 692 | a | U | U | C | U | C | U | C | C | A | U | G | U | C | A | c | C | G | C | 71 | 2 | 14 | c | false | <90% | 744 | ||
| NM_006020 | ALKBH1 | 1810 | 1828 | U | U | U | C | U | C | U | a | C | A | U | G | U | C | A | U | u | u | C | 11 | 3 | 8 | c | false | <90% | 2585 | ||
| NM_021230 | MLL3 | 11970 | 11988 | g | U | U | C | a | C | U | C | C | A | a | G | U | C | A | U | C | G | C | -14 | 3 | 8 | c | false | <90% | 14358 | ||
| NM_170606 | MLL3 | 14484 | 14502 | g | U | U | C | a | C | U | C | C | A | a | G | U | C | A | U | C | G | C | -14 | 3 | 8 | c | false | <90% | 16872 | ||
| NM_032136 | TKTL2 | 1753 | 1771 | U | U | U | C | U | g | U | C | C | g | U | G | U | C | A | U | C | G | a | -51 | 3 | 8 | bc | false | <90% | 2837 | ||
3 prime UTR Seed matches
Hits to same gene : 0
Hits to other genes : 0
View matched accessions
3 prime seed match details
| Accession | Gene name | Hits to this gene |
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