Automatic recommendation
Not OK - siRNA is not specific
22 hits were found for GCAGAGUCCUCAAUCUUAA (12 guide strand hits and 10 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_080872 | UNC5D | 1448 | 1466 | a | C | A | G | A | G | U | C | C | U | C | A | c | U | C | U | U | u | A | 84 | 3 | 11 | false | <90% | 7002 | |||
| NM_014890 | FILIP1L | 2298 | 2316 | a | g | A | G | A | G | U | C | C | U | C | A | c | U | C | U | U | A | c | 71 | 4 | 10 | false | <90% | 3274 | |||
| NM_182909 | FILIP1L | 3235 | 3253 | a | g | A | G | A | G | U | C | C | U | C | A | c | U | C | U | U | A | c | 71 | 4 | 10 | false | <90% | 3962 | |||
| NM_001042459 | FILIP1L | 3235 | 3253 | a | g | A | G | A | G | U | C | C | U | C | A | c | U | C | U | U | A | c | 71 | 4 | 10 | false | <90% | 4211 | |||
| NM_006024 | TAX1BP1 | 1979 | 1997 | c | C | A | G | A | G | U | C | C | U | C | A | A | U | g | U | U | u | c | 65 | 4 | 13 | c | false | <90% | 3466 | ||
| NM_178837 | C19orf51 | 1854 | 1872 | c | u | A | G | A | G | U | C | C | U | C | A | A | U | u | U | U | A | u | 56 | 4 | 12 | c | false | <90% | 2210 | ||
| NM_017780 | CHD7 | 9373 | 9391 | G | C | A | G | A | G | U | C | C | U | C | c | c | U | C | U | U | A | g | 50 | 3 | 11 | false | <90% | 10469 | |||
| NM_000857 | GUCY1B3 | 255 | 273 | G | C | A | a | A | G | U | C | C | U | C | A | A | U | C | U | c | A | A | 39 | 2 | 12 | c | false | <90% | 2443 | ||
| NM_003917 | AP1G2 | 2571 | 2589 | u | C | A | G | A | a | U | C | C | U | C | A | A | U | C | c | U | A | A | 8 | 3 | 9 | c | false | <90% | 2876 | ||
| NM_080545 | AP1G2 | 2994 | 3012 | u | C | A | G | A | a | U | C | C | U | C | A | A | U | C | c | U | A | A | 8 | 3 | 9 | c | false | <90% | 3305 | ||
| NM_153018 | ZFP3 | 4840 | 4858 | G | C | A | c | A | G | g | C | C | U | C | A | A | U | C | U | U | A | A | -3 | 2 | 12 | bc | false | <90% | 5011 | ||
| NM_018246 | CCDC25 | 1341 | 1359 | G | C | A | G | A | G | g | C | C | U | C | c | A | U | C | U | U | A | g | -5 | 3 | 6 | false | <90% | 3653 | |||
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_181354 | OXR1 | 1994 | 2012 | a | a | A | A | G | A | U | U | G | A | G | G | A | g | U | C | U | G | a | 62 | 4 | 11 | c | false | <90% | 4411 | ||
| NM_001077349 | ZNF682 | 2922 | 2940 | a | g | A | A | G | A | U | U | G | A | G | G | A | C | a | C | U | G | a | 56 | 4 | 12 | c | false | <90% | 3164 | ||
| NM_033196 | ZNF682 | 2965 | 2983 | a | g | A | A | G | A | U | U | G | A | G | G | A | C | a | C | U | G | a | 56 | 4 | 12 | c | false | <90% | 3207 | ||
| NM_199072 | MDFIC | 2706 | 2724 | a | g | A | A | G | A | U | U | G | A | G | u | A | C | U | C | U | G | a | 47 | 4 | 9 | false | <90% | 4607 | |||
| NM_032127 | C11orf56 | 2751 | 2769 | a | U | A | A | G | A | U | U | G | A | G | a | A | C | U | u | U | G | C | 38 | 3 | 10 | false | <90% | 3432 | |||
| NM_006788 | RALBP1 | 3892 | 3910 | a | g | g | A | G | A | U | U | G | A | G | u | A | C | U | C | U | G | C | 33 | 4 | 8 | false | <90% | 4368 | |||
| NM_134431 | SLCO1A2 | 3545 | 3563 | c | U | A | A | G | A | U | U | c | A | G | G | A | C | U | C | U | u | u | 30 | 4 | 8 | c | false | <90% | 4832 | ||
| NM_174914 | UGT3A2 | 958 | 976 | c | c | A | A | G | u | U | U | G | A | G | G | A | C | U | C | U | G | g | 18 | 4 | 12 | bc | false | <90% | 2341 | ||
| NM_006731 | FCMD | 1966 | 1984 | U | U | A | A | G | A | U | U | G | u | G | G | A | g | U | C | U | G | a | -7 | 3 | 9 | c | false | <90% | 7364 | ||
| NM_001079802 | FCMD | 2058 | 2076 | U | U | A | A | G | A | U | U | G | u | G | G | A | g | U | C | U | G | a | -7 | 3 | 9 | c | false | <90% | 7456 | ||
3 prime UTR Seed matches
Hits to same gene : 0
Hits to other genes : 2081
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