Automatic recommendation
OK - siRNA is specific for both sense and antisense (guide) strands
18 hits were found for GGAAAGAAUUUGACCUAGA (13 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_000123 | ERCC5 | 3568 | 3586 | a | G | A | A | A | G | A | A | U | U | U | G | A | g | C | U | A | c | u | 70 | 4 | 12 | c | false | <90% | 4100 | ||
| NR_002836 | PGM5P2 | 707 | 725 | G | a | c | A | A | G | A | A | U | U | U | G | A | C | C | U | A | G | A | 69 | 2 | 16 | bc | false | <90% | 1988 | ||
| NM_021965 | PGM5 | 759 | 777 | G | a | c | A | A | G | A | A | U | U | U | G | A | C | C | U | A | G | A | 69 | 2 | 16 | bc | false | <90% | 3341 | ||
| XR_019133 | LOC646903 | 1657 | 1675 | u | G | A | A | A | G | A | A | U | U | U | G | A | C | C | a | A | c | A | 69 | 3 | 14 | c | false | <90% | 1978 | ||
| XR_017284 | LOC646903 | 1657 | 1675 | u | G | A | A | A | G | A | A | U | U | U | G | A | C | C | a | A | c | A | 69 | 3 | 14 | c | false | <90% | 1978 | ||
| NM_001014986 | FOLH1 | 560 | 578 | G | G | A | A | A | G | A | A | U | U | U | G | g | C | C | U | g | G | A | 66 | 2 | 12 | false | <90% | 2560 | |||
| NM_004476 | FOLH1 | 560 | 578 | G | G | A | A | A | G | A | A | U | U | U | G | g | C | C | U | g | G | A | 66 | 2 | 12 | false | <90% | 2653 | |||
| XM_942521 | USP24 | 5483 | 5501 | u | a | g | A | A | G | A | A | U | U | U | G | A | C | C | U | A | a | A | 64 | 4 | 14 | c | false | <90% | 10051 | ||
| XM_371254 | USP24 | 5501 | 5519 | u | a | g | A | A | G | A | A | U | U | U | G | A | C | C | U | A | a | A | 64 | 4 | 14 | c | false | <90% | 10069 | ||
| NM_002772 | PRSS7 | 1743 | 1761 | u | u | c | A | A | G | A | A | U | U | U | G | A | C | u | U | A | G | A | 42 | 4 | 11 | c | false | <90% | 3696 | ||
| NM_152379 | C1orf131 | 525 | 543 | c | a | c | A | A | G | A | A | U | U | U | a | A | C | C | U | A | G | A | 33 | 4 | 8 | false | <90% | 1486 | |||
| NM_025040 | ZNF614 | 2248 | 2266 | u | G | A | A | A | u | A | A | U | U | U | G | c | C | C | U | A | G | A | 24 | 3 | 6 | false | <90% | 4627 | |||
| NM_016081 | PALLD | 5168 | 5186 | a | a | A | A | A | u | A | A | U | U | U | G | A | C | C | U | A | G | u | 18 | 4 | 12 | bc | false | <90% | 5809 | ||
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_001081676 | SCN3A | 7096 | 7114 | U | u | U | A | G | G | U | C | A | A | A | U | g | C | U | U | U | C | C | 78 | 2 | 10 | false | <90% | 8994 | |||
| NM_001081677 | SCN3A | 7096 | 7114 | U | u | U | A | G | G | U | C | A | A | A | U | g | C | U | U | U | C | C | 78 | 2 | 10 | false | <90% | 8994 | |||
| NM_006922 | SCN3A | 7243 | 7261 | U | u | U | A | G | G | U | C | A | A | A | U | g | C | U | U | U | C | C | 78 | 2 | 10 | false | <90% | 9141 | |||
| NM_002463 | MX2 | 2591 | 2609 | U | C | U | g | G | G | U | C | A | A | A | U | U | C | U | U | c | u | u | 32 | 4 | 12 | c | false | <90% | 2961 | ||
| NM_006920 | SCN1A | 2063 | 2081 | a | g | a | A | G | G | U | C | A | A | g | U | U | C | U | U | U | C | C | 5 | 4 | 8 | c | false | <90% | 8100 | ||
3 prime UTR Seed matches
Hits to same gene : 0
Hits to other genes : 3507
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