Automatic recommendation
Not OK - siRNA is not specific
15 hits were found for UGGCAAAUGUUGUGAGAAA (10 guide strand hits and 5 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_014705 | DOCK4 | 4064 | 4082 | a | G | G | C | A | A | A | U | G | U | U | G | g | G | A | G | A | A | u | 82 | 3 | 11 | false | <90% | 8343 | |||
| NM_024613 | PLEKHF2 | 2809 | 2827 | g | G | G | g | A | A | A | U | G | U | U | G | U | G | A | G | A | u | A | 58 | 3 | 13 | c | false | <90% | 2905 | ||
| NM_004972 | JAK2 | 468 | 486 | c | G | G | C | A | A | A | U | G | U | U | c | U | G | A | a | A | A | A | 38 | 3 | 10 | false | <90% | 5097 | |||
| NM_148954 | PSMB9 | 335 | 353 | c | u | G | C | A | A | A | U | G | U | g | G | U | G | A | G | A | A | A | 25 | 3 | 8 | c | false | <90% | 1018 | ||
| NM_002800 | PSMB9 | 365 | 383 | c | u | G | C | A | A | A | U | G | U | g | G | U | G | A | G | A | A | A | 25 | 3 | 8 | c | false | <90% | 1048 | ||
| NM_017811 | UBE2R2 | 4116 | 4134 | g | G | G | C | A | c | A | U | G | U | U | G | U | a | A | G | A | A | A | 15 | 3 | 7 | c | false | <90% | 4457 | ||
| NM_152588 | TMTC2 | 4631 | 4649 | g | G | G | u | A | A | A | U | G | U | a | G | U | G | A | G | A | A | A | 0 | 3 | 8 | c | false | <90% | 4855 | ||
| NM_014841 | SNAP91 | 3494 | 3512 | c | u | u | C | A | A | c | U | G | U | U | G | U | G | A | G | A | A | A | 0 | 4 | 12 | bc | false | <90% | 4369 | ||
| NM_001004128 | QSOX1 | 740 | 758 | a | G | G | C | c | A | A | U | G | U | g | G | U | G | A | G | A | A | A | -14 | 3 | 8 | c | false | <90% | 2583 | ||
| NM_002826 | QSOX1 | 740 | 758 | a | G | G | C | c | A | A | U | G | U | g | G | U | G | A | G | A | A | A | -14 | 3 | 8 | c | false | <90% | 3316 | ||
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_000390 | CHM | 3682 | 3700 | U | U | U | C | U | C | A | C | A | A | C | A | U | c | U | G | g | C | c | 51 | 3 | 13 | c | false | <90% | 5442 | ||
| NM_174916 | UBR1 | 4970 | 4988 | g | U | U | C | U | C | A | g | A | A | C | A | U | U | U | G | C | u | g | 28 | 4 | 9 | c | false | <90% | 7758 | ||
| XM_932802 | LOC645307 | 963 | 981 | g | U | U | C | a | C | A | C | A | A | C | A | U | U | U | c | C | C | A | 20 | 3 | 10 | c | false | <90% | 3875 | ||
| NM_000129 | F13A1 | 3719 | 3737 | a | a | U | C | U | C | A | C | A | g | C | A | U | U | U | G | C | C | A | 3 | 3 | 9 | bc | false | <90% | 3863 | ||
| NM_017754 | C6orf107 | 8635 | 8653 | U | U | U | C | U | C | u | C | A | A | u | A | U | U | U | G | C | C | u | -32 | 3 | 7 | c | false | <90% | 9658 | ||
3 prime UTR Seed matches
Hits to same gene : 0
Hits to other genes : 2852
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