Automatic recommendation
Not OK - siRNA is not specific
20 hits were found for UCUCAUAGCAUUUGAUUAC (15 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_058191 | C21orf66 | 1721 | 1739 | U | C | U | C | A | U | A | G | C | A | U | U | U | G | A | U | U | A | u | 95 | 1 | 18 | abc | false | <90% | 2530 | ||
| XM_944303 | SETD5 | 1590 | 1608 | c | a | c | C | A | U | A | G | C | A | U | U | U | G | A | U | U | A | u | 62 | 4 | 15 | bc | false | <90% | 6306 | ||
| XM_931455 | SETD5 | 1590 | 1608 | c | a | c | C | A | U | A | G | C | A | U | U | U | G | A | U | U | A | u | 62 | 4 | 15 | bc | false | <90% | 6306 | ||
| XM_931478 | SETD5 | 1319 | 1337 | c | a | c | C | A | U | A | G | C | A | U | U | U | G | A | U | U | A | u | 62 | 4 | 15 | bc | false | <90% | 6556 | ||
| XM_944276 | SETD5 | 1320 | 1338 | c | a | c | C | A | U | A | G | C | A | U | U | U | G | A | U | U | A | u | 62 | 4 | 15 | bc | false | <90% | 6557 | ||
| XM_944298 | SETD5 | 1590 | 1608 | c | a | c | C | A | U | A | G | C | A | U | U | U | G | A | U | U | A | u | 62 | 4 | 15 | bc | false | <90% | 6575 | ||
| XM_931447 | SETD5 | 1590 | 1608 | c | a | c | C | A | U | A | G | C | A | U | U | U | G | A | U | U | A | u | 62 | 4 | 15 | bc | false | <90% | 6575 | ||
| NM_001080517 | SETD5 | 1590 | 1608 | c | a | c | C | A | U | A | G | C | A | U | U | U | G | A | U | U | A | u | 62 | 4 | 15 | bc | false | <90% | 6827 | ||
| XM_939712 | SETD5 | 1590 | 1608 | c | a | c | C | A | U | A | G | C | A | U | U | U | G | A | U | U | A | u | 62 | 4 | 15 | bc | false | <90% | 6827 | ||
| XM_944295 | SETD5 | 1590 | 1608 | c | a | c | C | A | U | A | G | C | A | U | U | U | G | A | U | U | A | u | 62 | 4 | 15 | bc | false | <90% | 7060 | ||
| XM_931444 | SETD5 | 1590 | 1608 | c | a | c | C | A | U | A | G | C | A | U | U | U | G | A | U | U | A | u | 62 | 4 | 15 | bc | false | <90% | 7060 | ||
| XM_944260 | SETD5 | 1834 | 1852 | c | a | c | C | A | U | A | G | C | A | U | U | U | G | A | U | U | A | u | 62 | 4 | 15 | bc | false | <90% | 7071 | ||
| XM_931376 | SETD5 | 1873 | 1891 | c | a | c | C | A | U | A | G | C | A | U | U | U | G | A | U | U | A | u | 62 | 4 | 15 | bc | false | <90% | 7110 | ||
| NM_015163 | TRIM9 | 2394 | 2412 | U | C | c | C | A | U | A | G | C | A | U | U | U | G | A | U | a | A | C | 56 | 2 | 13 | c | false | <90% | 4571 | ||
| NM_203301 | FBXO33 | 2348 | 2366 | U | C | U | g | A | U | A | G | C | A | U | U | U | c | A | U | U | A | a | 38 | 3 | 9 | c | false | <90% | 3742 | ||
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_019610 | RBMXL1 | 2635 | 2653 | G | a | A | A | U | C | A | A | A | U | G | C | U | A | a | G | A | G | u | 58 | 3 | 12 | c | false | <90% | 3877 | ||
| NM_198887 | NUP43 | 2258 | 2276 | u | U | A | A | U | C | A | A | A | U | G | a | U | A | U | G | A | u | c | 56 | 4 | 10 | false | <90% | 3862 | |||
| NM_002267 | KPNA3 | 2751 | 2769 | G | U | A | A | U | C | A | A | A | U | G | C | U | g | U | G | c | a | u | 49 | 4 | 13 | c | false | <90% | 4471 | ||
| NM_006851 | GLIPR1 | 3574 | 3592 | u | U | A | A | U | g | A | A | A | U | G | C | U | A | a | G | A | G | A | 9 | 3 | 8 | c | false | <90% | 3924 | ||
| NM_006101 | NDC80 | 793 | 811 | a | c | c | A | U | a | A | A | A | U | G | C | U | A | U | G | A | G | A | 3 | 4 | 13 | bc | false | <90% | 2150 | ||
3 prime UTR Seed matches
Hits to same gene : 0
Hits to other genes : 1661
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