Automatic recommendation
OK - siRNA is specific for both sense and antisense (guide) strands
18 hits were found for GACUCUCAGCAAUGUCAAC (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_021097 | SLC8A1 | 1503 | 1521 | G | c | a | U | C | U | C | A | G | C | A | A | U | G | U | C | A | A | a | 64 | 3 | 15 | bc | false | <90% | 6053 | ||
| NM_053067 | UBQLN1 | 1539 | 1557 | c | A | C | U | a | U | C | A | G | C | A | A | U | G | U | C | A | A | a | 41 | 3 | 13 | bc | false | <90% | 2354 | ||
| NM_013438 | UBQLN1 | 1708 | 1726 | c | A | C | U | a | U | C | A | G | C | A | A | U | G | U | C | A | A | a | 41 | 3 | 13 | bc | false | <90% | 3952 | ||
| NM_153234 | LIX1 | 2296 | 2314 | G | A | a | U | g | U | C | A | G | C | A | A | U | G | U | C | A | A | u | 23 | 3 | 13 | bc | false | <90% | 3913 | ||
| NM_001496 | GFRA3 | 1049 | 1067 | c | u | u | U | g | U | C | A | G | C | A | A | U | G | U | C | A | A | C | 15 | 4 | 14 | bc | false | <90% | 1980 | ||
| NM_144985 | CDH24 | 834 | 852 | c | A | C | g | C | U | C | A | G | C | g | A | U | G | U | C | A | A | C | 0 | 3 | 8 | c | false | <90% | 2759 | ||
| NM_022478 | CDH24 | 834 | 852 | c | A | C | g | C | U | C | A | G | C | g | A | U | G | U | C | A | A | C | 0 | 3 | 8 | c | false | <90% | 2873 | ||
| NM_006467 | POLR3G | 1890 | 1908 | G | A | C | U | C | U | C | A | G | a | A | A | U | G | c | C | A | A | a | -12 | 3 | 9 | c | false | <90% | 3285 | ||
| NM_145739 | OSBPL6 | 467 | 485 | G | A | C | U | C | U | C | A | G | u | c | A | U | G | U | C | A | A | u | -49 | 3 | 9 | c | false | <90% | 3548 | ||
| NM_032523 | OSBPL6 | 788 | 806 | G | A | C | U | C | U | C | A | G | u | c | A | U | G | U | C | A | A | u | -49 | 3 | 9 | c | false | <90% | 3794 | ||
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 | |||||||||||||
| XM_001129806 | LOC729269 | 1929 | 1947 | u | U | U | G | A | C | A | U | U | G | C | U | G | A | G | A | a | g | g | 66 | 4 | 15 | ac | false | <90% | 3075 | ||
| XM_943874 | MICAL3 | 1929 | 1947 | u | U | U | G | A | C | A | U | U | G | C | U | G | A | G | A | a | g | g | 66 | 4 | 15 | ac | false | <90% | 3075 | ||
| NM_014897 | ZNF652 | 3364 | 3382 | c | a | U | G | A | C | A | U | U | G | C | U | G | A | u | A | G | U | g | 56 | 4 | 12 | c | false | <90% | 5428 | ||
| NM_020374 | C12orf4 | 949 | 967 | u | U | U | G | A | g | A | U | U | G | C | U | G | A | G | A | G | c | a | 27 | 4 | 11 | c | false | <90% | 3830 | ||
| XM_941451 | EHBP1L1 | 821 | 839 | G | a | U | G | A | C | u | U | U | G | C | U | G | A | G | A | G | U | g | 17 | 3 | 11 | bc | false | <90% | 3151 | ||
| XM_170658 | EHBP1L1 | 821 | 839 | G | a | U | G | A | C | u | U | U | G | C | U | G | A | G | A | G | U | g | 17 | 3 | 11 | bc | false | <90% | 5185 | ||
| NM_022143 | LRRC4 | 2384 | 2402 | G | U | U | G | A | a | A | U | U | G | C | U | G | A | G | A | u | a | a | 5 | 4 | 10 | c | false | <90% | 3723 | ||
| NM_006206 | PDGFRA | 3713 | 3731 | a | a | g | G | A | C | A | U | U | G | g | U | G | A | G | A | G | U | C | 5 | 4 | 8 | c | false | <90% | 6405 | ||
3 prime UTR Seed matches
Hits to same gene : 0
Hits to other genes : 1286
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