Automatic recommendation
OK - siRNA is specific for both sense and antisense (guide) strands
17 hits were found for GCAUGAAGUACCCUGGAUU (10 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_006095 | ATP8A1 | 2759 | 2777 | u | g | u | U | G | A | A | G | U | A | C | C | C | U | G | a | A | U | U | 40 | 4 | 12 | c | false | <90% | 3794 | ||
| NM_145322 | OSBPL3 | 5652 | 5670 | G | C | A | a | G | A | A | G | U | A | C | C | C | a | G | G | A | U | g | 38 | 3 | 9 | c | false | <90% | 6529 | ||
| NM_145321 | OSBPL3 | 5745 | 5763 | G | C | A | a | G | A | A | G | U | A | C | C | C | a | G | G | A | U | g | 38 | 3 | 9 | c | false | <90% | 6622 | ||
| NM_145320 | OSBPL3 | 5760 | 5778 | G | C | A | a | G | A | A | G | U | A | C | C | C | a | G | G | A | U | g | 38 | 3 | 9 | c | false | <90% | 6637 | ||
| NM_015550 | OSBPL3 | 5853 | 5871 | G | C | A | a | G | A | A | G | U | A | C | C | C | a | G | G | A | U | g | 38 | 3 | 9 | c | false | <90% | 6730 | ||
| NM_001040102 | TMEM10 | 3116 | 3134 | u | C | A | U | G | A | A | G | g | A | C | C | u | U | G | G | A | U | U | 27 | 3 | 7 | false | <90% | 3521 | |||
| NM_033207 | TMEM10 | 3185 | 3203 | u | C | A | U | G | A | A | G | g | A | C | C | u | U | G | G | A | U | U | 27 | 3 | 7 | false | <90% | 3590 | |||
| NM_001040103 | TMEM10 | 3224 | 3242 | u | C | A | U | G | A | A | G | g | A | C | C | u | U | G | G | A | U | U | 27 | 3 | 7 | false | <90% | 3629 | |||
| NM_002912 | REV3L | 2194 | 2212 | c | u | A | U | G | A | A | a | U | A | C | C | C | U | G | G | A | U | c | 19 | 4 | 10 | bc | false | <90% | 10716 | ||
| NR_002723 | GABPAP | 99260 | 99278 | G | C | A | a | G | A | A | G | U | u | C | C | C | U | G | G | A | U | U | -19 | 2 | 9 | bc | false | <90% | 194142 | ||
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_017786 | FLJ20366 | 23 | 41 | A | u | g | g | C | A | G | G | G | U | A | C | U | U | C | A | U | G | C | 32 | 3 | 15 | bc | false | <90% | 3430 | ||
| NM_014483 | RBMS3 | 1120 | 1138 | g | g | U | C | C | A | G | a | G | U | A | C | U | U | C | A | U | G | g | 19 | 4 | 10 | bc | false | <90% | 1600 | ||
| NM_001003793 | RBMS3 | 1120 | 1138 | g | g | U | C | C | A | G | a | G | U | A | C | U | U | C | A | U | G | g | 19 | 4 | 10 | bc | false | <90% | 2817 | ||
| NM_014215 | INSRR | 3121 | 3139 | A | A | U | C | C | A | G | a | G | U | A | C | U | U | C | A | g | c | g | 6 | 4 | 8 | c | false | <90% | 4148 | ||
| XR_016672 | LOC441238 | 222 | 240 | A | A | U | C | C | A | G | G | G | a | A | C | U | U | C | u | U | G | C | -8 | 2 | 9 | c | false | <90% | 1493 | ||
| NM_015938 | NMD3 | 341 | 359 | A | A | U | C | C | A | G | G | G | a | A | C | U | U | C | u | U | G | C | -8 | 2 | 9 | c | false | <90% | 2758 | ||
| NM_005613 | RGS4 | 1509 | 1527 | c | A | U | C | C | A | a | G | G | a | A | C | U | U | C | A | U | G | C | -51 | 3 | 9 | bc | false | <90% | 2769 | ||
3 prime UTR Seed matches
Hits to same gene : 0
Hits to other genes : 1836
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