Automatic recommendation
OK - siRNA is specific for both sense and antisense (guide) strands
18 hits were found for CCUUGAUGUUAGAUGGAGA (10 guide strand hits and 8 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_152629 | GLIS3 | 4057 | 4075 | g | C | U | U | G | A | U | G | U | U | A | G | A | U | G | G | g | a | u | 66 | 4 | 15 | ac | false | <90% | 6672 | ||
| NM_001042413 | GLIS3 | 5041 | 5059 | g | C | U | U | G | A | U | G | U | U | A | G | A | U | G | G | g | a | u | 66 | 4 | 15 | ac | false | <90% | 7656 | ||
| NM_198584 | CA13 | 1503 | 1521 | C | a | g | U | G | A | U | G | U | U | A | G | A | U | G | G | A | a | A | 66 | 3 | 14 | c | false | <90% | 3564 | ||
| NM_080617 | CBLN4 | 1198 | 1216 | a | C | U | U | G | A | U | G | U | U | A | a | A | U | G | G | A | a | A | 61 | 3 | 10 | false | <90% | 2573 | |||
| NM_004415 | DSP | 5429 | 5447 | a | C | U | U | G | A | U | G | U | U | A | G | A | a | G | a | A | G | A | 52 | 3 | 12 | c | false | <90% | 9730 | ||
| NM_005902 | SMAD3 | 3226 | 3244 | u | u | c | U | G | A | U | G | U | U | A | G | A | g | G | G | A | G | A | 47 | 4 | 10 | c | false | <90% | 6256 | ||
| NM_020865 | DHX36 | 3250 | 3268 | a | C | U | U | G | A | U | G | U | U | A | u | A | U | G | u | A | G | A | 38 | 3 | 10 | false | <90% | 3600 | |||
| NM_001008394 | EID3 | 1202 | 1220 | u | u | c | U | G | A | a | G | U | U | A | G | A | U | G | G | A | G | A | 0 | 4 | 12 | bc | false | <90% | 1447 | ||
| XR_017445 | LOC391081 | 836 | 854 | C | C | U | U | G | A | U | u | c | U | A | G | A | U | G | G | A | G | c | -27 | 3 | 9 | bc | false | <90% | 1373 | ||
| XR_019377 | LOC391081 | 836 | 854 | C | C | U | U | G | A | U | u | c | U | A | G | A | U | G | G | A | G | c | -27 | 3 | 9 | bc | false | <90% | 1373 | ||
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 | |||||||||||||
| XR_017771 | LOC554208 | 1084 | 1102 | U | C | U | C | C | A | U | C | U | A | A | g | c | U | C | A | A | G | a | 50 | 3 | 11 | false | <90% | 2018 | |||
| XR_018023 | LOC442523 | 1084 | 1102 | U | C | U | C | C | A | U | C | U | A | A | g | c | U | C | A | A | G | a | 50 | 3 | 11 | false | <90% | 2018 | |||
| XR_016777 | LOC442523 | 1084 | 1102 | U | C | U | C | C | A | U | C | U | A | A | g | c | U | C | A | A | G | a | 50 | 3 | 11 | false | <90% | 2018 | |||
| NM_173812 | DPY19L2 | 3119 | 3137 | U | C | U | C | C | A | U | C | U | A | A | g | c | U | C | A | A | G | a | 50 | 3 | 11 | false | <90% | 4064 | |||
| NM_005142 | GIF | 968 | 986 | U | C | U | g | C | A | U | C | U | A | A | C | A | U | C | A | c | u | G | 37 | 3 | 12 | c | false | <90% | 1536 | ||
| NM_017440 | MDM1 | 1714 | 1732 | U | C | U | C | C | A | U | C | U | A | A | g | A | U | g | A | A | G | c | 36 | 3 | 11 | false | <90% | 2936 | |||
| XR_016239 | LOC643014 | 50 | 68 | U | C | U | C | C | A | U | C | U | u | A | g | A | U | C | A | A | G | u | -21 | 3 | 9 | false | <90% | 859 | |||
| XR_018450 | LOC648960 | 50 | 68 | U | C | U | C | C | A | U | C | U | u | A | g | A | U | C | A | A | G | u | -21 | 3 | 9 | false | <90% | 859 | |||
3 prime UTR Seed matches
Hits to same gene : 0
Hits to other genes : 1774
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