Automatic recommendation
OK - siRNA is specific for both sense and antisense (guide) strands
18 hits were found for UUAUUAUGAGAUGUUGGCU (12 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 | |||||||||||||
| NM_003474 | ADAM12 | 4388 | 4406 | a | U | A | U | U | A | U | G | A | G | A | U | G | c | U | G | G | C | U | 78 | 2 | 12 | c | false | <90% | 5504 | ||
| NM_006750 | SNTB2 | 4017 | 4035 | U | U | A | a | U | A | U | G | A | G | A | U | G | U | U | G | a | a | U | 37 | 3 | 12 | c | false | <90% | 9771 | ||
| NM_020760 | HECW2 | 6597 | 6615 | c | U | A | U | U | A | U | G | g | G | A | U | G | U | U | G | G | C | a | 32 | 3 | 9 | bc | false | <90% | 6926 | ||
| NM_001025100 | MBP | 4809 | 4827 | U | U | A | U | U | A | U | G | A | G | c | U | u | U | U | G | G | C | U | 28 | 2 | 10 | false | <90% | 4889 | |||
| XM_001130164 | MGAM | 3786 | 3804 | g | U | A | U | g | A | U | G | A | G | A | U | G | g | U | G | G | C | U | 27 | 3 | 8 | c | false | <90% | 3948 | ||
| XM_936233 | LOC642103 | 75 | 93 | g | U | A | U | g | A | U | G | A | G | A | U | G | g | U | G | G | C | U | 27 | 3 | 8 | c | false | <90% | 4557 | ||
| XM_936233 | LOC642103 | 2769 | 2787 | g | U | A | U | g | A | U | G | A | G | A | U | G | g | U | G | G | C | U | 27 | 3 | 8 | c | false | <90% | 4557 | ||
| NM_004668 | MGAM | 3840 | 3858 | g | U | A | U | g | A | U | G | A | G | A | U | G | g | U | G | G | C | U | 27 | 3 | 8 | c | false | <90% | 6513 | ||
| NM_005006 | NDUFS1 | 2582 | 2600 | a | a | A | U | U | A | U | G | A | G | u | U | G | U | U | G | G | C | U | 25 | 3 | 8 | c | false | <90% | 3417 | ||
| NM_001007246 | BRWD1 | 726 | 744 | U | U | A | U | U | c | U | G | A | G | A | U | G | U | U | G | u | u | U | 10 | 3 | 10 | c | false | <90% | 2488 | ||
| NM_002662 | PLD1 | 3702 | 3720 | U | U | A | U | U | A | U | u | A | G | A | U | G | U | U | G | u | a | a | 6 | 4 | 8 | c | false | <90% | 5494 | ||
| NM_032446 | MEGF10 | 3877 | 3895 | U | U | A | U | U | g | U | a | A | G | A | U | G | U | U | G | G | C | U | -25 | 2 | 11 | bc | false | <90% | 7522 | ||
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_152587 | C11orf65 | 400 | 418 | A | G | C | a | u | A | C | A | U | C | U | C | A | U | A | A | U | A | A | 11 | 2 | 14 | bc | false | <90% | 1033 | ||
| NM_032165 | LRRIQ1 | 1283 | 1301 | A | G | C | C | A | A | C | A | g | C | U | a | A | U | A | A | U | A | A | 6 | 2 | 8 | false | <90% | 4457 | |||
| NM_001079910 | LRRIQ1 | 1283 | 1301 | A | G | C | C | A | A | C | A | g | C | U | a | A | U | A | A | U | A | A | 6 | 2 | 8 | false | <90% | 5460 | |||
| NM_016489 | NT5C3 | 251 | 269 | g | c | C | C | A | A | C | A | U | g | U | C | A | U | A | A | U | A | u | -1 | 4 | 8 | bc | false | <90% | 1552 | ||
| NM_001002010 | NT5C3 | 387 | 405 | g | c | C | C | A | A | C | A | U | g | U | C | A | U | A | A | U | A | u | -1 | 4 | 8 | bc | false | <90% | 1688 | ||
| NM_001002009 | NT5C3 | 442 | 460 | g | c | C | C | A | A | C | A | U | g | U | C | A | U | A | A | U | A | u | -1 | 4 | 8 | bc | false | <90% | 1743 | ||
3 prime UTR Seed matches
Hits to same gene : 0
Hits to other genes : 4015
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