Automatic recommendation
OK - siRNA is specific for both sense and antisense (guide) strands
19 hits were found for GAUCCAGCAUCUAGAGACC (12 guide strand hits and 7 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_001125694 | LOC727742 | 795 | 813 | u | A | U | C | C | A | G | C | A | U | C | U | g | G | A | G | A | u | g | 79 | 4 | 11 | false | <90% | 2609 | |||
| NM_004522 | KIF5C | 1445 | 1463 | u | A | U | C | C | A | G | C | A | U | C | U | g | G | A | G | A | u | g | 79 | 4 | 11 | false | <90% | 6927 | |||
| NM_021636 | LGR6 | 550 | 568 | c | A | U | C | C | A | G | C | A | U | C | U | g | G | g | G | A | C | C | 62 | 3 | 11 | false | <90% | 3345 | |||
| NM_001017403 | LGR6 | 663 | 681 | c | A | U | C | C | A | G | C | A | U | C | U | g | G | g | G | A | C | C | 62 | 3 | 11 | false | <90% | 3458 | |||
| NM_013385 | PSCD4 | 2462 | 2480 | G | u | c | C | C | A | G | C | A | U | C | U | c | G | A | G | A | C | C | 58 | 3 | 9 | false | <90% | 3221 | |||
| NM_007337 | DLEC1 | 2832 | 2850 | c | u | g | C | C | A | G | C | A | U | C | U | g | G | A | G | A | C | C | 56 | 4 | 9 | false | <90% | 5508 | |||
| NM_007335 | DLEC1 | 2832 | 2850 | c | u | g | C | C | A | G | C | A | U | C | U | g | G | A | G | A | C | C | 56 | 4 | 9 | false | <90% | 5632 | |||
| NM_000360 | TH | 346 | 364 | a | A | U | C | C | A | c | C | A | U | C | U | A | G | A | G | A | C | C | 31 | 2 | 12 | bc | false | <90% | 1817 | ||
| NM_199293 | TH | 427 | 445 | a | A | U | C | C | A | c | C | A | U | C | U | A | G | A | G | A | C | C | 31 | 2 | 12 | bc | false | <90% | 1898 | ||
| NM_199292 | TH | 439 | 457 | a | A | U | C | C | A | c | C | A | U | C | U | A | G | A | G | A | C | C | 31 | 2 | 12 | bc | false | <90% | 1910 | ||
| NM_001077497 | PRR3 | 1069 | 1087 | G | A | U | C | C | A | G | C | c | U | g | U | A | G | A | G | A | C | u | -26 | 3 | 8 | c | false | <90% | 2778 | ||
| NM_025263 | PRR3 | 1132 | 1150 | G | A | U | C | C | A | G | C | c | U | g | U | A | G | A | G | A | C | u | -26 | 3 | 8 | c | false | <90% | 2841 | ||
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_181893 | UBE2D3 | 41 | 59 | c | G | U | C | U | g | U | A | G | A | U | G | C | U | G | G | A | g | a | 27 | 4 | 11 | c | false | <90% | 2006 | ||
| NM_181890 | UBE2D3 | 70 | 88 | c | G | U | C | U | g | U | A | G | A | U | G | C | U | G | G | A | g | a | 27 | 4 | 11 | c | false | <90% | 2187 | ||
| NM_004127 | GPS1 | 1066 | 1084 | u | G | U | C | U | C | a | A | G | A | U | G | C | U | G | G | A | c | g | 24 | 4 | 10 | c | false | <90% | 1880 | ||
| NM_212492 | GPS1 | 1549 | 1567 | u | G | U | C | U | C | a | A | G | A | U | G | C | U | G | G | A | c | g | 24 | 4 | 10 | c | false | <90% | 2363 | ||
| NM_144767 | AKAP13 | 6062 | 6080 | G | u | g | C | U | C | U | A | G | u | U | G | C | U | G | G | A | U | C | -13 | 3 | 9 | bc | false | <90% | 8081 | ||
| NM_007200 | AKAP13 | 11271 | 11289 | G | u | g | C | U | C | U | A | G | u | U | G | C | U | G | G | A | U | C | -13 | 3 | 9 | bc | false | <90% | 13290 | ||
| NM_006738 | AKAP13 | 11283 | 11301 | G | u | g | C | U | C | U | A | G | u | U | G | C | U | G | G | A | U | C | -13 | 3 | 9 | bc | false | <90% | 13302 | ||
3 prime UTR Seed matches
Hits to same gene : 0
Hits to other genes : 1400
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