Automatic recommendation
Not OK - siRNA is not specific
29 hits were found for GAGACAAUGCAGAGGAGUA (20 guide strand hits and 9 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_173589 | C11orf47 | 1366 | 1384 | c | u | G | A | C | A | A | U | G | C | A | G | A | G | G | A | G | g | A | 83 | 3 | 15 | ac | false | <90% | 3222 | ||
NM_001001438 | LSS | 2452 | 2470 | a | u | c | A | C | A | A | U | G | C | A | G | A | G | G | A | G | U | c | 62 | 4 | 15 | bc | false | <90% | 2658 | ||
XR_018322 | LOC401602 | 1375 | 1393 | u | u | G | A | C | A | A | U | G | C | A | G | A | u | G | A | G | U | u | 62 | 4 | 11 | c | false | <90% | 2798 | ||
XR_016272 | LOC401602 | 1375 | 1393 | u | u | G | A | C | A | A | U | G | C | A | G | A | u | G | A | G | U | u | 62 | 4 | 11 | c | false | <90% | 2798 | ||
NM_001282 | AP2B1 | 1565 | 1583 | u | u | G | A | C | A | A | U | G | C | A | G | A | u | G | A | G | U | u | 62 | 4 | 11 | c | false | <90% | 5730 | ||
NM_001030006 | AP2B1 | 1565 | 1583 | u | u | G | A | C | A | A | U | G | C | A | G | A | u | G | A | G | U | u | 62 | 4 | 11 | c | false | <90% | 5772 | ||
NM_002472 | MYH8 | 4865 | 4883 | G | A | G | A | C | A | A | U | G | C | A | G | A | G | c | A | c | g | c | 44 | 4 | 14 | c | false | <90% | 6016 | ||
NM_014423 | AFF4 | 1606 | 1624 | a | A | G | A | C | A | A | U | G | C | c | G | A | G | G | A | G | U | A | 36 | 2 | 9 | c | false | <90% | 9580 | ||
XR_016955 | LOC645615 | 894 | 912 | a | A | G | A | C | A | A | a | G | C | A | G | A | G | G | A | G | g | g | 28 | 4 | 9 | c | false | <90% | 1800 | ||
XR_018878 | LOC645615 | 894 | 912 | a | A | G | A | C | A | A | a | G | C | A | G | A | G | G | A | G | g | g | 28 | 4 | 9 | c | false | <90% | 1800 | ||
NM_006894 | FMO3 | 207 | 225 | c | A | G | A | C | c | A | U | G | C | A | G | A | G | G | A | G | g | g | 27 | 4 | 11 | c | false | <90% | 2053 | ||
NM_001002294 | FMO3 | 224 | 242 | c | A | G | A | C | c | A | U | G | C | A | G | A | G | G | A | G | g | g | 27 | 4 | 11 | c | false | <90% | 2070 | ||
NM_002373 | MAP1A | 2149 | 2167 | u | A | G | A | C | A | c | U | G | C | A | G | A | G | G | A | G | g | g | 24 | 4 | 10 | c | false | <90% | 10275 | ||
XM_001132518 | LOC728819 | 692 | 710 | c | A | G | A | a | A | A | U | G | C | A | G | A | G | G | A | u | U | A | 23 | 3 | 11 | c | false | <90% | 1172 | ||
XM_001133308 | LOC731364 | 692 | 710 | c | A | G | A | a | A | A | U | G | C | A | G | A | G | G | A | u | U | A | 23 | 3 | 11 | c | false | <90% | 1172 | ||
NM_006011 | ST8SIA2 | 2014 | 2032 | a | u | G | A | C | A | A | U | G | a | A | G | A | G | G | A | G | U | A | 3 | 3 | 9 | bc | false | <90% | 5626 | ||
NM_023010 | UPF3B | 1609 | 1627 | G | g | u | A | C | A | c | U | G | C | A | G | A | G | G | A | G | U | A | 2 | 3 | 12 | bc | false | <90% | 2342 | ||
NM_080632 | UPF3B | 1648 | 1666 | G | g | u | A | C | A | c | U | G | C | A | G | A | G | G | A | G | U | A | 2 | 3 | 12 | bc | false | <90% | 2381 | ||
NM_001253 | CDC5L | 588 | 606 | G | A | G | A | C | A | A | U | G | a | A | G | A | G | G | A | a | a | c | -13 | 4 | 9 | c | false | <90% | 3012 | ||
NM_019044 | CCDC93 | 3059 | 3077 | a | A | G | A | g | A | g | U | G | C | A | G | A | G | G | A | G | U | A | -19 | 3 | 12 | bc | false | <90% | 6794 |
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_013372 | GREM1 | 1644 | 1662 | a | A | C | U | C | C | U | C | U | G | C | u | U | U | G | U | C | c | C | 61 | 3 | 10 | false | <90% | 4175 | |||
NM_001011645 | AR | 1405 | 1423 | U | A | C | U | C | C | U | C | U | G | C | A | g | U | G | c | C | U | u | 58 | 3 | 12 | false | <90% | 1765 | |||
NM_000044 | AR | 3954 | 3972 | U | A | C | U | C | C | U | C | U | G | C | A | g | U | G | c | C | U | u | 58 | 3 | 12 | false | <90% | 4314 | |||
NM_145176 | SLC2A12 | 1207 | 1225 | c | A | u | U | C | C | U | C | U | G | C | A | U | U | G | g | C | U | C | 52 | 3 | 12 | c | false | <90% | 5599 | ||
NM_002615 | SERPINF1 | 171 | 189 | U | A | C | U | C | C | U | C | U | G | C | A | U | U | G | g | a | g | C | 47 | 3 | 15 | c | false | <90% | 1542 | ||
NM_024032 | C17orf53 | 2556 | 2574 | g | c | u | U | C | C | U | C | U | G | C | u | U | U | G | U | C | U | C | 33 | 4 | 8 | false | <90% | 2727 | |||
NM_007332 | TRPA1 | 470 | 488 | U | A | C | c | C | C | U | C | U | G | C | A | U | U | G | U | g | c | u | 32 | 4 | 12 | c | false | <90% | 5190 | ||
NM_001013660 | FRRS1 | 1333 | 1351 | U | u | a | U | C | C | U | u | U | G | C | A | U | U | G | U | C | U | C | 6 | 3 | 11 | bc | false | <90% | 2678 | ||
NR_002140 | OR6W1P | 807 | 825 | g | u | u | U | C | C | U | C | U | c | C | A | U | U | G | U | C | U | C | -15 | 4 | 9 | bc | false | <90% | 1502 |
3 prime UTR Seed matches
Hits to same gene : 0
Hits to other genes : 1902
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