Automatic recommendation
Not OK - siRNA is not specific
22 hits were found for GGUUUCCUCAUAAAGAGAA (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_133370 | YTHDC1 | 1368 | 1386 | u | u | U | U | U | C | C | U | C | A | U | A | A | A | G | A | G | u | A | 83 | 3 | 15 | ac | false | <90% | 6195 | ||
| NM_001031732 | YTHDC1 | 1422 | 1440 | u | u | U | U | U | C | C | U | C | A | U | A | A | A | G | A | G | u | A | 83 | 3 | 15 | ac | false | <90% | 6249 | ||
| NM_022754 | SFXN1 | 2891 | 2909 | a | a | U | U | U | C | C | U | C | A | U | A | A | A | G | A | a | A | A | 63 | 3 | 14 | ac | false | <90% | 2986 | ||
| NM_016248 | AKAP11 | 8224 | 8242 | a | a | a | U | U | C | C | U | C | A | U | A | u | A | G | A | G | A | A | 56 | 4 | 9 | false | <90% | 9919 | |||
| NM_015113 | ZZEF1 | 1436 | 1454 | a | G | U | U | U | C | C | U | C | A | U | A | A | g | G | A | u | A | A | 54 | 3 | 12 | c | false | <90% | 11412 | ||
| NM_002547 | OPHN1 | 2745 | 2763 | u | c | U | U | U | C | C | a | C | A | U | A | A | A | G | A | G | A | c | 19 | 4 | 10 | bc | false | <90% | 7350 | ||
| NM_018025 | GPATCH1 | 2854 | 2872 | a | G | g | U | U | C | C | U | C | A | a | A | A | A | G | A | G | A | A | 17 | 3 | 8 | c | false | <90% | 3390 | ||
| NM_138395 | MARS2 | 2270 | 2288 | G | G | U | U | U | C | C | U | g | A | U | A | A | A | a | A | G | A | g | 10 | 3 | 8 | c | false | <90% | 3043 | ||
| NM_025054 | VCPIP1 | 2718 | 2736 | G | G | U | U | U | C | C | U | C | c | U | A | A | A | G | A | G | u | u | 9 | 3 | 9 | c | false | <90% | 8192 | ||
| NM_022123 | NPAS3 | 3145 | 3163 | G | G | U | U | U | C | u | U | C | A | U | A | A | A | G | A | u | c | u | 2 | 4 | 9 | c | false | <90% | 3428 | ||
| XM_001127447 | LOC728431 | 462 | 480 | u | a | c | U | U | C | u | U | C | A | U | A | A | A | G | A | G | A | A | 0 | 4 | 12 | bc | false | <90% | 1088 | ||
| XM_001132105 | LOC732178 | 462 | 480 | u | a | c | U | U | C | u | U | C | A | U | A | A | A | G | A | G | A | A | 0 | 4 | 12 | bc | false | <90% | 1088 | ||
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_014635 | GCC2 | 2076 | 2094 | g | U | C | U | C | U | U | U | A | U | G | A | G | G | A | A | A | a | C | 95 | 2 | 16 | ac | false | <90% | 6833 | ||
| NM_181453 | GCC2 | 2161 | 2179 | g | U | C | U | C | U | U | U | A | U | G | A | G | G | A | A | A | a | C | 95 | 2 | 16 | ac | false | <90% | 6918 | ||
| NM_001987 | ETV6 | 4596 | 4614 | U | g | u | U | C | U | U | U | A | U | G | A | G | a | A | A | A | C | C | 49 | 3 | 10 | c | false | <90% | 5992 | ||
| NM_003750 | EIF3S10 | 2453 | 2471 | g | U | C | U | g | U | U | U | A | U | G | A | G | G | A | A | A | a | a | 38 | 4 | 12 | c | false | <90% | 5305 | ||
| NM_032883 | TOX2 | 2333 | 2351 | g | U | C | U | a | U | U | U | A | U | G | A | a | G | A | A | A | C | C | 36 | 3 | 7 | false | <90% | 2533 | |||
| XM_001128700 | LOC728883 | 779 | 797 | U | U | C | U | C | U | U | g | A | U | G | A | G | G | A | A | A | g | a | 30 | 3 | 9 | c | false | <90% | 1050 | ||
| XM_001127767 | LOC730930 | 779 | 797 | U | U | C | U | C | U | U | g | A | U | G | A | G | G | A | A | A | g | a | 30 | 3 | 9 | c | false | <90% | 1050 | ||
| NM_002169 | IFNA5 | 523 | 541 | U | U | C | U | C | U | U | U | A | U | c | A | G | c | A | A | A | C | u | 14 | 3 | 10 | c | false | <90% | 570 | ||
| NM_002519 | NPAT | 2054 | 2072 | c | U | C | U | C | U | U | U | A | g | G | A | G | G | A | A | A | u | g | 7 | 4 | 8 | c | false | <90% | 5895 | ||
| NM_053055 | THEM4 | 2098 | 2116 | c | U | C | U | u | U | U | U | A | U | a | A | G | G | A | A | A | C | C | -14 | 3 | 8 | c | false | <90% | 2224 | ||
3 prime UTR Seed matches
Hits to same gene : 0
Hits to other genes : 2035
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