Automatic recommendation
OK - siRNA is specific for both sense and antisense (guide) strands
14 hits were found for AGGAGCAAGUCUGCUAUGC (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_001006600 | ERBB2IP | 3042 | 3060 | A | G | G | A | G | C | A | A | G | U | C | U | G | C | c | A | c | a | C | 49 | 3 | 14 | c | false | <90% | 6709 | ||
| NM_018695 | ERBB2IP | 3042 | 3060 | A | G | G | A | G | C | A | A | G | U | C | U | G | C | c | A | c | a | C | 49 | 3 | 14 | c | false | <90% | 6916 | ||
| NM_181773 | APOBEC3H | 15 | 33 | A | G | G | g | G | C | A | A | G | U | C | U | G | C | U | A | a | G | g | 34 | 3 | 12 | c | false | <90% | 916 | ||
| NM_016319 | COPS7A | 1446 | 1464 | g | G | G | A | G | C | c | A | G | U | C | U | G | C | c | A | U | G | C | 6 | 3 | 7 | c | false | <90% | 1868 | ||
| NM_001001685 | FLJ45079 | 747 | 765 | A | G | G | A | a | C | A | A | G | c | C | U | G | C | U | A | U | G | C | -34 | 2 | 9 | bc | false | <90% | 4678 | ||
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_003777 | DNAH11 | 4628 | 4646 | a | C | A | U | A | G | C | A | G | A | C | U | U | G | g | U | C | a | U | 70 | 3 | 13 | c | false | <90% | 14188 | ||
| NM_022746 | MOSC1 | 599 | 617 | a | a | A | U | A | G | C | A | G | A | C | U | U | G | u | U | C | C | g | 56 | 4 | 12 | c | false | <90% | 2043 | ||
| XM_001133864 | LOXL1 | 1613 | 1631 | G | C | A | c | A | G | C | A | G | A | C | U | U | c | C | U | C | C | c | 38 | 3 | 9 | c | false | <90% | 2353 | ||
| NM_005576 | LOXL1 | 1625 | 1643 | G | C | A | c | A | G | C | A | G | A | C | U | U | c | C | U | C | C | c | 38 | 3 | 9 | c | false | <90% | 2361 | ||
| NM_015194 | MYO1D | 908 | 926 | u | C | A | U | A | G | C | A | G | A | a | U | U | G | C | U | C | u | c | 29 | 4 | 9 | c | false | <90% | 5182 | ||
| NM_182703 | ANKDD1A | 1044 | 1062 | a | C | A | U | A | G | C | A | G | A | u | a | U | G | C | U | C | C | U | 2 | 3 | 9 | false | <90% | 3126 | |||
| NM_001024463 | HISPPD2A | 2390 | 2408 | G | C | A | c | A | G | C | A | G | A | g | U | U | G | C | U | C | C | g | -3 | 3 | 7 | c | false | <90% | 4920 | ||
| NM_014659 | HISPPD2A | 2390 | 2408 | G | C | A | c | A | G | C | A | G | A | g | U | U | G | C | U | C | C | g | -3 | 3 | 7 | c | false | <90% | 5565 | ||
| NM_004751 | GCNT3 | 979 | 997 | G | C | A | U | g | G | a | A | G | A | C | U | U | G | C | U | C | C | a | -22 | 3 | 11 | bc | false | <90% | 2128 | ||
3 prime UTR Seed matches
Hits to same gene : 0
Hits to other genes : 2664
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