Automatic recommendation
Warning - siRNA is specific for only the antisense (guide) strand
13 hits were found for CAGAAAGAGUACAACAGAU (6 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 | |||||||||||||
| NM_001040666 | STEAP2 | 1445 | 1463 | g | A | G | g | A | A | G | A | G | U | A | C | u | A | C | A | G | A | U | 50 | 3 | 8 | false | <90% | 2320 | |||
| NM_001040665 | STEAP2 | 1427 | 1445 | g | A | G | g | A | A | G | A | G | U | A | C | u | A | C | A | G | A | U | 50 | 3 | 8 | false | <90% | 6708 | |||
| NM_152999 | STEAP2 | 1651 | 1669 | g | A | G | g | A | A | G | A | G | U | A | C | u | A | C | A | G | A | U | 50 | 3 | 8 | false | <90% | 6932 | |||
| NM_207361 | FREM2 | 14217 | 14235 | C | A | G | g | A | A | G | A | G | U | A | C | A | u | C | A | G | A | a | 38 | 3 | 9 | c | false | <90% | 16179 | ||
| NM_001067 | TOP2A | 3603 | 3621 | a | A | G | A | A | A | G | A | G | U | c | C | A | u | C | A | G | A | U | 17 | 3 | 9 | c | false | <90% | 5698 | ||
| NM_001778 | CD48 | 330 | 348 | C | A | G | A | A | A | G | A | G | g | A | C | A | A | C | A | G | c | a | 9 | 3 | 9 | c | false | <90% | 1099 | ||
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_013367 | ANAPC4 | 845 | 863 | A | U | C | U | G | U | U | G | U | A | C | U | C | U | U | U | C | U | u | 95 | 1 | 18 | abc | false | <90% | 2701 | ||
| NM_022054 | KCNK13 | 2194 | 2212 | g | U | C | U | G | U | U | G | U | A | C | U | C | U | U | U | a | U | a | 69 | 3 | 15 | ac | false | <90% | 2517 | ||
| NM_002707 | PPM1G | 2096 | 2114 | c | U | C | U | G | U | U | G | U | A | C | a | C | U | U | U | C | a | a | 56 | 4 | 10 | false | <90% | 2165 | |||
| NM_177983 | PPM1G | 2196 | 2214 | c | U | C | U | G | U | U | G | U | A | C | a | C | U | U | U | C | a | a | 56 | 4 | 10 | false | <90% | 2265 | |||
| NM_016451 | COPB1 | 3226 | 3244 | A | U | C | U | u | U | U | G | U | A | C | U | C | U | U | U | C | a | u | 40 | 3 | 12 | c | false | <90% | 3528 | ||
| NM_017515 | SLC35F2 | 1072 | 1090 | u | U | u | U | G | U | U | G | g | A | C | U | C | U | U | U | C | U | G | 18 | 3 | 10 | bc | false | <90% | 2954 | ||
| NM_018639 | WSB2 | 1580 | 1598 | A | a | g | U | G | U | U | G | a | A | C | U | C | U | U | U | C | U | G | 8 | 3 | 10 | bc | false | <90% | 2833 | ||
3 prime UTR Seed matches
Hits to same gene : 0
Hits to other genes : 3527
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