Automatic recommendation
OK - siRNA is specific for both sense and antisense (guide) strands
16 hits were found for GAAAAACCAAACGUAACAC (10 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 | |||||||||||||
| XM_936273 | ZSWIM6 | 3419 | 3437 | u | A | A | A | A | A | C | C | A | A | A | C | a | a | A | A | C | A | C | 68 | 3 | 11 | false | <90% | 4907 | |||
| NM_022465 | IKZF4 | 3936 | 3954 | u | A | A | A | A | A | C | C | A | A | A | C | a | c | A | A | C | A | C | 68 | 3 | 11 | false | <90% | 5506 | |||
| XM_035299 | ZSWIM6 | 4058 | 4076 | u | A | A | A | A | A | C | C | A | A | A | C | a | a | A | A | C | A | C | 68 | 3 | 11 | false | <90% | 5545 | |||
| NM_139017 | IL31RA | 704 | 722 | u | A | A | A | A | A | C | C | A | A | A | C | G | U | A | c | a | A | C | 48 | 3 | 14 | c | false | <90% | 2393 | ||
| XM_001129292 | MBOAT2 | 7496 | 7514 | G | A | A | A | A | A | C | C | A | A | A | a | G | U | u | A | C | A | g | 36 | 3 | 11 | false | <90% | 8428 | |||
| NM_033224 | PURB | 1070 | 1088 | a | A | A | A | A | A | C | a | A | A | A | C | G | U | A | A | C | A | C | 35 | 2 | 11 | bc | false | <90% | 9074 | ||
| NM_033418 | C1orf156 | 1035 | 1053 | a | g | g | A | A | A | C | C | A | A | A | a | G | U | A | A | C | A | C | 33 | 4 | 8 | false | <90% | 1445 | |||
| NM_003073 | SMARCB1 | 416 | 434 | a | A | A | A | A | A | C | a | A | A | A | C | c | U | A | A | C | A | C | 25 | 3 | 6 | false | <90% | 1717 | |||
| NM_014757 | MAML1 | 3597 | 3615 | a | A | A | A | A | A | C | C | A | A | c | a | G | U | A | A | C | A | C | 2 | 3 | 9 | false | <90% | 5745 | |||
| XM_001126853 | MAML1 | 3091 | 3109 | a | A | A | A | A | A | C | C | A | A | c | a | G | U | A | A | C | A | C | 2 | 3 | 9 | false | <90% | 6146 | |||
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_018050 | MANSC1 | 1985 | 2003 | G | U | u | U | U | A | u | G | U | U | U | G | G | U | U | U | U | U | g | 9 | 3 | 11 | bc | false | <90% | 2297 | ||
| NM_005822 | DSCR1L1 | 2144 | 2162 | u | U | G | U | U | A | C | G | U | g | U | G | a | U | U | U | U | U | C | 4 | 3 | 8 | false | <90% | 3318 | |||
| NM_016489 | NT5C3 | 1393 | 1411 | G | U | G | U | U | A | g | G | U | U | U | G | G | U | U | a | U | U | u | 2 | 3 | 8 | c | false | <90% | 1552 | ||
| NM_001002010 | NT5C3 | 1529 | 1547 | G | U | G | U | U | A | g | G | U | U | U | G | G | U | U | a | U | U | u | 2 | 3 | 8 | c | false | <90% | 1688 | ||
| NM_001002009 | NT5C3 | 1584 | 1602 | G | U | G | U | U | A | g | G | U | U | U | G | G | U | U | a | U | U | u | 2 | 3 | 8 | c | false | <90% | 1743 | ||
| NM_003371 | VAV2 | 4405 | 4423 | G | U | G | U | U | u | g | G | U | U | U | G | G | U | U | U | U | U | g | -34 | 3 | 11 | bc | false | <90% | 4707 | ||
3 prime UTR Seed matches
Hits to same gene : 0
Hits to other genes : 3190
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