Automatic recommendation
OK - siRNA is specific for both sense and antisense (guide) strands
15 hits were found for UUUCGGAAGAAACAGGUAC (10 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_145858 | CRYZL1 | 806 | 824 | g | U | U | u | G | G | A | A | G | A | A | A | C | A | G | G | U | g | g | 53 | 4 | 13 | c | false | <90% | 1726 | ||
| NM_000615 | NCAM1 | 5187 | 5205 | g | U | U | a | G | G | A | A | G | A | A | A | C | A | G | G | U | c | a | 53 | 4 | 13 | c | false | <90% | 5951 | ||
| NM_181351 | NCAM1 | 5217 | 5235 | g | U | U | a | G | G | A | A | G | A | A | A | C | A | G | G | U | c | a | 53 | 4 | 13 | c | false | <90% | 5981 | ||
| NM_007345 | ZNF236 | 36 | 54 | U | U | U | a | G | G | A | A | G | A | A | A | g | A | G | G | U | A | a | 47 | 3 | 8 | false | <90% | 8140 | |||
| NM_001001389 | CD44 | 1480 | 1498 | c | a | a | C | G | G | A | A | G | A | A | A | C | A | G | c | U | A | C | 40 | 4 | 12 | c | false | <90% | 5619 | ||
| NM_000610 | CD44 | 1609 | 1627 | c | a | a | C | G | G | A | A | G | A | A | A | C | A | G | c | U | A | C | 40 | 4 | 12 | c | false | <90% | 5748 | ||
| NM_002589 | PCDH7 | 782 | 800 | U | U | U | C | G | G | A | A | G | A | A | g | C | A | G | G | a | g | g | 35 | 4 | 11 | false | <90% | 4646 | |||
| NM_032457 | PCDH7 | 782 | 800 | U | U | U | C | G | G | A | A | G | A | A | g | C | A | G | G | a | g | g | 35 | 4 | 11 | false | <90% | 4893 | |||
| NM_032456 | PCDH7 | 782 | 800 | U | U | U | C | G | G | A | A | G | A | A | g | C | A | G | G | a | g | g | 35 | 4 | 11 | false | <90% | 4921 | |||
| NM_023008 | FLJ12949 | 886 | 904 | U | U | U | C | u | G | A | A | G | A | A | A | C | A | G | G | a | g | g | 17 | 4 | 11 | c | false | <90% | 3023 | ||
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_031272 | TEX14 | 2832 | 2850 | G | a | A | C | C | U | G | U | U | U | C | U | U | C | u | G | A | A | A | 63 | 2 | 12 | c | false | <90% | 4825 | ||
| NM_198393 | TEX14 | 2832 | 2850 | G | a | A | C | C | U | G | U | U | U | C | U | U | C | u | G | A | A | A | 63 | 2 | 12 | c | false | <90% | 4945 | ||
| NM_001004461 | OR10A6 | 177 | 195 | G | U | A | C | C | U | G | U | U | U | C | U | c | C | u | G | A | A | c | 59 | 3 | 12 | false | <90% | 945 | |||
| NM_032944 | STK31 | 341 | 359 | G | U | A | C | C | c | G | U | U | U | C | U | U | C | C | a | A | A | u | 5 | 3 | 9 | c | false | <90% | 3616 | ||
| NM_013316 | CNOT4 | 3256 | 3274 | G | U | A | C | C | U | c | U | U | U | C | U | U | C | a | G | A | A | u | 4 | 3 | 7 | c | false | <90% | 3333 | ||
3 prime UTR Seed matches
Hits to same gene : 0
Hits to other genes : 385
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