Automatic recommendation
OK - siRNA is specific for both sense and antisense (guide) strands
18 hits were found for AAGAAGAACUCCCUCGCCU (9 guide strand hits and 9 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_206999 | CNOT1 | 4270 | 4288 | c | A | G | A | A | G | A | A | C | U | C | C | C | U | C | c | C | a | U | 69 | 3 | 14 | c | false | <90% | 5019 | ||
| NM_016284 | CNOT1 | 4270 | 4288 | c | A | G | A | A | G | A | A | C | U | C | C | C | U | C | c | C | a | U | 69 | 3 | 14 | c | false | <90% | 8449 | ||
| NM_006456 | ST6GALNAC2 | 649 | 667 | A | u | G | A | A | G | A | A | C | U | C | C | C | U | C | G | u | C | U | 65 | 2 | 14 | ac | false | <90% | 1908 | ||
| NM_003658 | BARX2 | 718 | 736 | A | A | G | A | A | G | A | A | C | U | C | C | a | U | C | c | C | C | a | 58 | 3 | 12 | false | <90% | 1455 | |||
| NM_021830 | PEO1 | 2520 | 2538 | A | A | c | A | A | G | A | A | C | U | C | C | C | U | C | a | C | C | U | 54 | 2 | 12 | c | false | <90% | 3630 | ||
| NM_152369 | SLC44A3 | 188 | 206 | A | A | G | A | A | G | A | A | C | U | C | C | C | c | C | G | u | g | g | 49 | 4 | 13 | c | false | <90% | 2098 | ||
| XM_001127121 | LOC728298 | 314 | 332 | c | A | G | A | A | G | c | A | C | U | C | C | g | U | C | G | C | C | U | 21 | 3 | 6 | false | <90% | 1317 | |||
| XM_937671 | LOC341112 | 29 | 47 | A | A | G | A | A | G | A | g | C | U | C | C | C | U | C | G | g | u | U | 11 | 3 | 8 | c | false | <90% | 675 | ||
| NM_033028 | BBS4 | 1196 | 1214 | A | A | G | A | A | G | A | A | C | g | C | C | C | U | g | G | C | C | c | -12 | 3 | 9 | c | false | <90% | 2482 | ||
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_012309 | SHANK2 | 3990 | 4008 | A | G | G | g | G | A | G | G | G | A | G | U | U | u | U | U | C | U | a | 38 | 3 | 9 | c | false | <90% | 8778 | ||
| NM_001175 | ARHGDIB | 1134 | 1152 | g | c | c | a | G | A | G | G | G | A | G | U | U | C | U | U | C | U | U | 30 | 4 | 15 | bc | false | <90% | 1216 | ||
| NM_001079839 | OCIAD1 | 413 | 431 | A | G | G | C | G | A | c | G | G | A | G | U | g | C | U | U | C | U | g | 18 | 3 | 6 | false | <90% | 2306 | |||
| NM_015052 | HECW1 | 4493 | 4511 | c | c | u | C | G | c | G | G | G | A | G | U | U | C | U | U | C | U | U | 3 | 4 | 13 | bc | false | <90% | 6839 | ||
| NM_172198 | KCND3 | 688 | 706 | c | G | G | a | G | A | a | G | G | A | G | U | U | C | U | U | C | U | U | -5 | 3 | 12 | bc | false | <90% | 2636 | ||
| NM_004980 | KCND3 | 688 | 706 | c | G | G | a | G | A | a | G | G | A | G | U | U | C | U | U | C | U | U | -5 | 3 | 12 | bc | false | <90% | 2693 | ||
| NM_001040627 | NCALD | 94 | 112 | A | G | G | C | G | A | G | u | G | A | u | U | U | C | U | U | C | U | g | -28 | 3 | 7 | c | false | <90% | 3586 | ||
| NM_001040629 | NCALD | 94 | 112 | A | G | G | C | G | A | G | u | G | A | u | U | U | C | U | U | C | U | g | -28 | 3 | 7 | c | false | <90% | 3642 | ||
| NM_001040626 | NCALD | 94 | 112 | A | G | G | C | G | A | G | u | G | A | u | U | U | C | U | U | C | U | g | -28 | 3 | 7 | c | false | <90% | 3673 | ||
3 prime UTR Seed matches
Hits to same gene : 0
Hits to other genes : 3835
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