Automatic recommendation
OK - siRNA is specific for both sense and antisense (guide) strands
14 hits were found for CUAUGGGAGUGGGCCUCAG (5 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_015338 | ASXL1 | 5835 | 5853 | C | U | A | U | G | G | G | A | G | U | G | G | G | C | a | U | C | u | c | 67 | 3 | 14 | c | false | <90% | 7047 | ||
| NM_001268 | RCBTB2 | 683 | 701 | C | U | A | U | G | G | G | A | G | U | G | G | u | C | C | a | C | A | u | 58 | 3 | 12 | false | <90% | 3204 | |||
| NM_006988 | ADAMTS1 | 2363 | 2381 | C | U | u | U | G | G | G | A | G | U | G | G | G | C | C | U | g | c | G | 54 | 3 | 13 | c | false | <90% | 4670 | ||
| NM_033643 | RPL36 | 86 | 104 | C | U | A | U | G | G | c | c | G | U | G | G | G | C | C | U | C | A | a | -33 | 3 | 10 | bc | false | <90% | 453 | ||
| NM_015414 | RPL36 | 190 | 208 | C | U | A | U | G | G | c | c | G | U | G | G | G | C | C | U | C | A | a | -33 | 3 | 10 | bc | false | <90% | 557 | ||
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_023923 | PHACTR4 | 3445 | 3463 | C | U | c | A | G | G | C | C | C | A | C | U | C | C | C | A | c | A | c | 51 | 3 | 13 | c | false | <90% | 6208 | ||
| NM_001048183 | PHACTR4 | 3462 | 3480 | C | U | c | A | G | G | C | C | C | A | C | U | C | C | C | A | c | A | c | 51 | 3 | 13 | c | false | <90% | 6225 | ||
| NM_012087 | GTF3C5 | 587 | 605 | C | U | G | A | G | G | C | C | C | A | C | U | C | C | g | A | g | g | u | 44 | 4 | 14 | c | false | <90% | 2380 | ||
| NM_023068 | SIGLEC1 | 1105 | 1123 | a | g | G | A | u | G | C | C | C | A | C | U | C | C | C | A | U | A | c | 30 | 4 | 13 | bc | false | <90% | 6736 | ||
| NM_147152 | ITSN2 | 697 | 715 | a | U | G | A | u | G | C | C | C | A | C | U | C | C | C | c | U | A | G | 20 | 3 | 10 | c | false | <90% | 4558 | ||
| NM_019595 | ITSN2 | 697 | 715 | a | U | G | A | u | G | C | C | C | A | C | U | C | C | C | c | U | A | G | 20 | 3 | 10 | c | false | <90% | 6027 | ||
| NM_006277 | ITSN2 | 697 | 715 | a | U | G | A | u | G | C | C | C | A | C | U | C | C | C | c | U | A | G | 20 | 3 | 10 | c | false | <90% | 6092 | ||
| NM_001006665 | RPS6KA1 | 787 | 805 | g | c | c | A | G | G | g | C | C | A | C | U | C | C | C | A | U | A | G | 0 | 4 | 12 | bc | false | <90% | 3112 | ||
| NM_002953 | RPS6KA1 | 874 | 892 | g | c | c | A | G | G | g | C | C | A | C | U | C | C | C | A | U | A | G | 0 | 4 | 12 | bc | false | <90% | 3199 | ||
3 prime UTR Seed matches
Hits to same gene : 0
Hits to other genes : 1171
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