Automatic recommendation
OK - siRNA is specific for both sense and antisense (guide) strands
16 hits were found for GCAAAUCAGCUAAAGCAAU (14 guide strand hits and 2 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_002271 | RANBP5 | 5142 | 5160 | G | C | c | A | A | U | C | A | G | C | U | A | g | A | G | C | A | A | U | 70 | 2 | 9 | false | <90% | 6019 | |||
| NM_198564 | FLJ44290 | 1067 | 1085 | u | C | A | A | A | U | C | A | G | C | U | A | A | A | G | g | A | u | c | 64 | 4 | 14 | c | false | <90% | 2048 | ||
| NM_015352 | POFUT1 | 3213 | 3231 | c | C | A | g | A | U | C | A | G | C | U | A | A | A | G | C | A | u | g | 53 | 4 | 13 | c | false | <90% | 5249 | ||
| NM_001010987 | IFIT1L | 1197 | 1215 | G | a | A | g | A | U | C | A | G | C | U | A | A | A | G | C | A | A | g | 46 | 3 | 14 | bc | false | <90% | 2005 | ||
| NM_003566 | EEA1 | 3146 | 3164 | a | u | A | A | A | U | g | A | G | C | U | A | A | A | G | C | A | A | U | 20 | 3 | 12 | bc | false | <90% | 8019 | ||
| XM_939505 | LOC285556 | 8510 | 8528 | G | u | A | A | A | U | a | A | G | C | U | A | A | A | G | C | A | A | a | 17 | 3 | 11 | bc | false | <90% | 10186 | ||
| XM_373030 | LOC285556 | 8510 | 8528 | G | u | A | A | A | U | a | A | G | C | U | A | A | A | G | C | A | A | a | 17 | 3 | 11 | bc | false | <90% | 10186 | ||
| NM_005139 | ANXA3 | 596 | 614 | G | C | A | A | A | g | C | A | G | C | U | A | A | A | G | a | A | A | U | 10 | 2 | 9 | c | false | <90% | 1634 | ||
| NM_031889 | ENAM | 2358 | 2376 | u | C | A | A | A | U | C | A | G | C | c | A | A | A | G | g | A | A | U | 10 | 3 | 9 | c | false | <90% | 5674 | ||
| NM_017948 | NOL8 | 3072 | 3090 | G | C | A | A | A | U | C | A | a | C | U | u | A | A | G | C | A | A | U | 6 | 2 | 8 | false | <90% | 4302 | |||
| XR_015273 | LOC728371 | 654 | 672 | c | C | A | A | A | U | C | A | G | a | U | A | A | A | u | C | A | A | U | -9 | 3 | 8 | c | false | <90% | 1648 | ||
| XR_015125 | LOC727770 | 859 | 877 | c | C | A | A | A | U | C | A | G | a | U | A | A | A | u | C | A | A | U | -9 | 3 | 8 | c | false | <90% | 1854 | ||
| XR_015744 | LOC730952 | 1486 | 1504 | c | C | A | A | A | U | C | A | G | a | U | A | A | A | u | C | A | A | U | -9 | 3 | 8 | c | false | <90% | 2485 | ||
| XR_017219 | LOC643854 | 129 | 147 | G | C | A | u | A | U | C | A | G | a | U | A | A | A | G | C | A | A | a | -24 | 3 | 8 | bc | false | <90% | 3894 | ||
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_173841 | IL1RN | 127 | 145 | A | U | g | G | C | U | U | U | A | G | C | U | G | A | c | U | U | G | u | 50 | 3 | 11 | c | false | <90% | 1865 | ||
| NM_015904 | EIF5B | 4362 | 4380 | A | U | U | u | C | U | U | U | A | G | C | U | G | c | U | U | U | G | u | 38 | 3 | 9 | c | false | <90% | 4698 | ||
3 prime UTR Seed matches
Hits to same gene : 0
Hits to other genes : 1404
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