Automatic recommendation
OK - siRNA is specific for both sense and antisense (guide) strands
13 hits were found for UACCACAUCAAAUGCAGCC (8 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_019065 | EFCBP2 | 618 | 636 | a | A | C | C | A | C | A | U | C | A | A | A | c | c | C | A | G | C | C | 68 | 3 | 11 | false | <90% | 1636 | |||
| NM_014641 | MDC1 | 5902 | 5920 | c | A | C | C | A | C | A | U | C | A | A | A | a | a | C | A | G | C | C | 68 | 3 | 11 | false | <90% | 7385 | |||
| XM_944501 | FLJ31033 | 95 | 113 | a | u | u | C | A | C | A | U | C | A | A | A | U | G | u | A | G | C | C | 42 | 4 | 11 | c | false | <90% | 6733 | ||
| XM_930988 | FLJ31033 | 233 | 251 | a | u | u | C | A | C | A | U | C | A | A | A | U | G | u | A | G | C | C | 42 | 4 | 11 | c | false | <90% | 6919 | ||
| NM_018128 | TSR1 | 3202 | 3220 | g | g | C | C | A | C | A | U | g | A | A | A | U | G | C | A | G | C | u | 21 | 4 | 9 | bc | false | <90% | 4890 | ||
| NM_002311 | LIG3 | 520 | 538 | U | A | C | C | A | C | A | U | u | A | A | A | U | G | C | A | u | g | u | 8 | 4 | 8 | c | false | <90% | 3059 | ||
| NM_013975 | LIG3 | 520 | 538 | U | A | C | C | A | C | A | U | u | A | A | A | U | G | C | A | u | g | u | 8 | 4 | 8 | c | false | <90% | 3701 | ||
| NM_180990 | LGICZ1 | 536 | 554 | g | A | C | C | A | C | A | g | C | A | A | c | U | G | C | A | G | C | C | 2 | 3 | 7 | false | <90% | 1289 | |||
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_006158 | NEFL | 3079 | 3097 | u | c | u | U | G | C | A | U | U | U | G | A | U | G | U | G | G | a | A | 64 | 4 | 14 | c | false | <90% | 3584 | ||
| NM_002586 | PBX2 | 2604 | 2622 | u | G | C | c | G | C | A | U | U | U | G | A | U | G | U | G | G | a | g | 53 | 4 | 13 | c | false | <90% | 3231 | ||
| NM_021947 | SRR | 1566 | 1584 | a | G | C | U | G | C | A | U | U | U | c | A | U | G | U | G | G | c | c | 29 | 4 | 9 | c | false | <90% | 2477 | ||
| NM_078476 | BTN2A1 | 1418 | 1436 | c | u | C | U | G | C | A | g | U | U | G | A | U | G | U | G | G | U | c | 19 | 4 | 10 | bc | false | <90% | 3129 | ||
| NM_130387 | ASB14 | 148 | 166 | G | G | C | U | G | g | A | U | U | U | G | A | U | G | U | G | a | a | c | 5 | 4 | 10 | c | false | <90% | 2218 | ||
3 prime UTR Seed matches
Hits to same gene : 0
Hits to other genes : 1473
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