Automatic recommendation
OK - siRNA is specific for both sense and antisense (guide) strands
16 hits were found for GAGCAUGGAAUAGAGACUC (5 guide strand hits and 11 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_031467 | SLC4A9 | 2139 | 2157 | c | c | G | C | A | U | G | G | A | A | U | A | c | A | G | A | C | U | g | 71 | 4 | 10 | false | <90% | 3118 | |||
| NM_153263 | ZNF549 | 415 | 433 | u | u | G | C | A | U | G | G | A | A | U | A | G | A | G | g | C | U | g | 55 | 4 | 13 | c | false | <90% | 3969 | ||
| NM_152636 | METT5D1 | 3616 | 3634 | a | A | G | C | A | U | G | G | A | A | U | A | G | A | u | u | C | U | C | 47 | 3 | 13 | c | false | <90% | 3959 | ||
| NM_172002 | HSCB | 471 | 489 | c | u | c | C | A | U | G | G | A | A | U | A | G | A | G | A | u | U | C | 43 | 4 | 13 | c | false | <90% | 1106 | ||
| NR_002936 | LOC222699 | 2523 | 2541 | G | A | G | C | c | U | G | G | A | A | U | A | G | A | u | A | C | U | u | 18 | 3 | 9 | c | false | <90% | 3623 | ||
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_014934 | DZIP1 | 5122 | 5140 | a | g | G | U | C | U | C | U | A | U | U | C | C | A | U | G | u | U | u | 58 | 4 | 14 | ac | false | <90% | 7457 | ||
| NM_198968 | DZIP1 | 5179 | 5197 | a | g | G | U | C | U | C | U | A | U | U | C | C | A | U | G | u | U | u | 58 | 4 | 14 | ac | false | <90% | 7514 | ||
| NM_002353 | TACSTD2 | 1310 | 1328 | G | A | G | U | C | U | C | U | A | U | U | C | C | A | g | G | g | c | C | 49 | 3 | 14 | c | false | <90% | 2805 | ||
| NR_003366 | ANKRD20B | 54327 | 54345 | c | A | G | U | C | U | C | U | A | U | U | C | C | A | U | c | g | U | C | 48 | 3 | 14 | c | false | <90% | 96524 | ||
| NM_005108 | XYLB | 2746 | 2764 | a | c | c | U | C | U | C | U | A | U | U | C | C | u | U | G | C | U | C | 47 | 4 | 10 | c | false | <90% | 3694 | ||
| NM_130389 | TRIM34 | 891 | 909 | a | A | G | a | C | U | g | U | A | U | U | C | C | A | U | G | C | U | C | -5 | 3 | 12 | bc | false | <90% | 2222 | ||
| NM_021616 | TRIM34 | 958 | 976 | a | A | G | a | C | U | g | U | A | U | U | C | C | A | U | G | C | U | C | -5 | 3 | 12 | bc | false | <90% | 2302 | ||
| NM_001003827 | TRIM34 | 982 | 1000 | a | A | G | a | C | U | g | U | A | U | U | C | C | A | U | G | C | U | C | -5 | 3 | 12 | bc | false | <90% | 2326 | ||
| NM_001003819 | TRIM6-TRIM34 | 2129 | 2147 | a | A | G | a | C | U | g | U | A | U | U | C | C | A | U | G | C | U | C | -5 | 3 | 12 | bc | false | <90% | 3490 | ||
| NM_020983 | ADCY6 | 3932 | 3950 | G | A | G | U | g | c | C | U | A | U | U | C | C | A | U | G | C | U | u | -19 | 3 | 12 | bc | false | <90% | 5877 | ||
| NM_015270 | ADCY6 | 4649 | 4667 | G | A | G | U | g | c | C | U | A | U | U | C | C | A | U | G | C | U | u | -19 | 3 | 12 | bc | false | <90% | 6594 | ||
3 prime UTR Seed matches
Hits to same gene : 0
Hits to other genes : 1606
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