Automatic recommendation
OK - siRNA is specific for both sense and antisense (guide) strands
15 hits were found for AUUGAAGGAAUGUAUGGAC (8 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_007347 | AP4E1 | 258 | 276 | g | a | U | G | A | A | G | G | A | A | U | G | U | A | U | G | G | u | g | 78 | 4 | 15 | ac | false | <90% | 6682 | ||
| NM_022058 | SLC4A10 | 2030 | 2048 | A | U | U | G | A | A | G | G | A | A | U | G | g | A | g | G | G | A | a | 59 | 3 | 12 | false | <90% | 3929 | |||
| NM_006281 | STK3 | 1671 | 1689 | A | U | U | G | A | A | G | G | A | A | U | a | U | u | U | G | G | A | u | 41 | 3 | 11 | false | <90% | 2826 | |||
| NM_139248 | LIPH | 500 | 518 | c | U | U | G | A | A | G | G | A | A | U | u | U | A | U | u | G | A | C | 38 | 3 | 10 | false | <90% | 2478 | |||
| NM_004458 | ACSL4 | 2304 | 2322 | A | U | U | G | A | A | c | G | A | A | U | G | U | A | U | G | G | g | g | 26 | 3 | 10 | c | false | <90% | 5043 | ||
| NM_022977 | ACSL4 | 2616 | 2634 | A | U | U | G | A | A | c | G | A | A | U | G | U | A | U | G | G | g | g | 26 | 3 | 10 | c | false | <90% | 5356 | ||
| NM_203372 | ACSL3 | 2481 | 2499 | A | U | U | G | A | g | c | G | A | A | U | G | U | A | U | G | G | A | a | -34 | 3 | 11 | bc | false | <90% | 4262 | ||
| NM_004457 | ACSL3 | 2588 | 2606 | A | U | U | G | A | g | c | G | A | A | U | G | U | A | U | G | G | A | a | -34 | 3 | 11 | bc | false | <90% | 4369 | ||
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_032044 | REG4 | 1239 | 1257 | G | g | C | C | A | U | A | C | A | U | U | C | C | U | U | u | A | A | U | 62 | 2 | 13 | c | false | <90% | 1285 | ||
| NM_001079877 | RASA4 | 4053 | 4071 | a | U | C | C | A | U | u | C | A | U | U | C | C | U | U | C | A | u | U | 29 | 3 | 10 | c | false | <90% | 5488 | ||
| NM_006989 | RASA4 | 4191 | 4209 | a | U | C | C | A | U | u | C | A | U | U | C | C | U | U | C | A | u | U | 29 | 3 | 10 | c | false | <90% | 5626 | ||
| XM_001127343 | LOC728372 | 423 | 441 | G | U | C | C | A | U | A | C | A | g | U | C | C | U | U | C | u | c | a | -13 | 4 | 9 | c | false | <90% | 591 | ||
| XR_018255 | LOC643004 | 1076 | 1094 | G | U | C | C | A | U | A | C | A | g | U | C | C | U | U | C | u | c | a | -13 | 4 | 9 | c | false | <90% | 2694 | ||
| NM_005722 | ACTR2 | 2136 | 2154 | c | U | C | C | c | U | A | C | A | g | U | C | C | U | U | C | A | A | U | -36 | 3 | 9 | bc | false | <90% | 3863 | ||
| NM_001005386 | ACTR2 | 2151 | 2169 | c | U | C | C | c | U | A | C | A | g | U | C | C | U | U | C | A | A | U | -36 | 3 | 9 | bc | false | <90% | 3878 | ||
3 prime UTR Seed matches
Hits to same gene : 0
Hits to other genes : 2158
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