Automatic recommendation
OK - siRNA is specific for both sense and antisense (guide) strands
26 hits were found for GGAUGUAAUGGAAGUGCUA (19 guide strand hits and 7 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_183376 | ARRDC4 | 1650 | 1668 | G | a | A | U | G | U | A | A | U | G | G | A | A | G | U | c | C | U | g | 57 | 3 | 13 | c | false | <90% | 4071 | ||
NM_023037 | FRY | 6214 | 6232 | u | u | A | U | G | U | A | A | U | G | G | A | A | G | c | G | C | U | c | 56 | 4 | 12 | c | false | <90% | 10718 | ||
NM_080921 | PTPRC | 1093 | 1111 | c | a | A | c | G | U | A | A | U | G | G | A | A | G | U | G | C | U | g | 44 | 4 | 14 | bc | false | <90% | 4847 | ||
NM_080922 | PTPRC | 1432 | 1450 | c | a | A | c | G | U | A | A | U | G | G | A | A | G | U | G | C | U | g | 44 | 4 | 14 | bc | false | <90% | 5186 | ||
NM_002838 | PTPRC | 1576 | 1594 | c | a | A | c | G | U | A | A | U | G | G | A | A | G | U | G | C | U | g | 44 | 4 | 14 | bc | false | <90% | 5330 | ||
NM_001042355 | CYLD | 1598 | 1616 | G | u | c | U | G | U | A | A | U | G | G | A | A | G | a | G | C | U | A | 44 | 3 | 11 | c | false | <90% | 8584 | ||
NM_001042412 | CYLD | 1622 | 1640 | G | u | c | U | G | U | A | A | U | G | G | A | A | G | a | G | C | U | A | 44 | 3 | 11 | c | false | <90% | 8608 | ||
NM_015247 | CYLD | 1744 | 1762 | G | u | c | U | G | U | A | A | U | G | G | A | A | G | a | G | C | U | A | 44 | 3 | 11 | c | false | <90% | 8730 | ||
XR_018354 | LOC646792 | 715 | 733 | G | u | g | a | G | U | A | A | U | G | G | A | A | G | U | G | C | U | u | 27 | 4 | 14 | bc | false | <90% | 879 | ||
XR_017300 | LOC646792 | 715 | 733 | G | u | g | a | G | U | A | A | U | G | G | A | A | G | U | G | C | U | u | 27 | 4 | 14 | bc | false | <90% | 879 | ||
NM_021729 | VPS11 | 1026 | 1044 | G | G | A | U | G | U | A | g | U | G | G | A | u | G | U | G | C | U | u | 22 | 3 | 7 | false | <90% | 3279 | |||
NM_006048 | UBE4B | 1298 | 1316 | G | a | u | U | u | U | A | A | U | G | G | A | A | G | U | G | C | U | A | 17 | 3 | 14 | bc | false | <90% | 5512 | ||
NM_014733 | ZFYVE16 | 3924 | 3942 | u | G | A | U | G | U | A | A | U | G | a | A | A | G | U | a | C | U | A | 10 | 3 | 9 | c | false | <90% | 6280 | ||
NM_019012 | PLEKHA5 | 2304 | 2322 | G | G | A | U | G | U | c | A | U | G | G | A | A | G | g | G | C | U | g | 4 | 3 | 7 | c | false | <90% | 4253 | ||
NM_006955 | ZNF33B | 5227 | 5245 | c | a | u | U | G | U | A | c | U | G | G | A | A | G | U | G | C | U | A | 4 | 4 | 11 | bc | false | <90% | 5958 | ||
NM_006974 | ZNF33A | 5385 | 5403 | c | a | u | U | G | U | A | c | U | G | G | A | A | G | U | G | C | U | A | 4 | 4 | 11 | bc | false | <90% | 6127 | ||
NM_006954 | ZNF33A | 5388 | 5406 | c | a | u | U | G | U | A | c | U | G | G | A | A | G | U | G | C | U | A | 4 | 4 | 11 | bc | false | <90% | 6130 | ||
NM_015350 | LRRC8B | 1881 | 1899 | a | a | c | U | G | a | A | A | U | G | G | A | A | G | U | G | C | U | A | 3 | 4 | 13 | bc | false | <90% | 3588 | ||
NM_014682 | ST18 | 2866 | 2884 | G | G | A | U | G | U | g | A | U | G | G | A | A | G | U | G | g | c | c | 2 | 4 | 9 | c | false | <90% | 6183 |
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_019109 | ALG1 | 1039 | 1057 | a | A | G | C | A | C | U | U | C | C | A | g | c | A | C | A | U | C | C | 53 | 3 | 10 | false | <90% | 2149 | |||
NM_022162 | NOD2 | 2256 | 2274 | a | A | G | C | A | C | U | U | C | C | A | c | U | c | C | A | U | C | C | 44 | 3 | 10 | false | <90% | 4485 | |||
NM_183374 | CYP26C1 | 1337 | 1355 | a | g | c | C | g | C | U | U | C | C | A | U | U | A | C | A | U | C | C | 15 | 4 | 14 | bc | false | <90% | 1569 | ||
NM_032129 | PLEKHN1 | 194 | 212 | a | A | G | C | u | C | U | U | C | C | A | c | U | A | C | A | U | C | C | 12 | 3 | 7 | false | <90% | 2418 | |||
NM_015540 | RPAP1 | 4472 | 4490 | g | A | G | C | c | C | U | a | C | C | A | U | U | A | C | A | U | C | C | -15 | 3 | 11 | bc | false | <90% | 4698 | ||
NM_003041 | SLC5A2 | 1372 | 1390 | c | A | G | C | u | C | U | U | C | g | A | U | U | A | C | A | U | C | C | -36 | 3 | 9 | bc | false | <90% | 2271 | ||
NM_022167 | XYLT2 | 886 | 904 | c | A | G | C | A | C | U | U | C | u | u | U | U | A | C | A | U | C | C | -46 | 3 | 8 | c | false | <90% | 3567 |
3 prime UTR Seed matches
Hits to same gene : 0
Hits to other genes : 1351
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