Automatic recommendation
OK - siRNA is specific for both sense and antisense (guide) strands
26 hits were found for UGCUGAAACGCGAGAGAAA (21 guide strand hits and 5 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_001271 | CHD2 | 3578 | 3596 | g | G | C | U | G | A | A | A | C | G | a | G | A | G | A | G | A | A | u | 31 | 3 | 9 | c | false | <90% | 9374 | ||
NM_201438 | PPHLN1 | 694 | 712 | U | G | C | U | G | A | A | A | a | G | C | u | A | G | A | G | A | A | A | 6 | 2 | 8 | false | <90% | 1338 | |||
NM_201440 | PPHLN1 | 694 | 712 | U | G | C | U | G | A | A | A | a | G | C | u | A | G | A | G | A | A | A | 6 | 2 | 8 | false | <90% | 1555 | |||
NM_201439 | PPHLN1 | 816 | 834 | U | G | C | U | G | A | A | A | a | G | C | u | A | G | A | G | A | A | A | 6 | 2 | 8 | false | <90% | 1677 | |||
NM_201515 | PPHLN1 | 859 | 877 | U | G | C | U | G | A | A | A | a | G | C | u | A | G | A | G | A | A | A | 6 | 2 | 8 | false | <90% | 1720 | |||
NM_016488 | PPHLN1 | 816 | 834 | U | G | C | U | G | A | A | A | a | G | C | u | A | G | A | G | A | A | A | 6 | 2 | 8 | false | <90% | 3483 | |||
NM_133378 | TTN | 78278 | 78296 | a | a | u | U | G | A | A | A | g | G | C | G | A | G | A | G | A | A | A | 6 | 4 | 10 | bc | false | <90% | 101519 | ||
NM_133437 | TTN | 59363 | 59381 | a | a | u | U | G | A | A | A | g | G | C | G | A | G | A | G | A | A | A | 6 | 4 | 10 | bc | false | <90% | 82604 | ||
NM_133432 | TTN | 59162 | 59180 | a | a | u | U | G | A | A | A | g | G | C | G | A | G | A | G | A | A | A | 6 | 4 | 10 | bc | false | <90% | 82403 | ||
NM_003319 | TTN | 58787 | 58805 | a | a | u | U | G | A | A | A | g | G | C | G | A | G | A | G | A | A | A | 6 | 4 | 10 | bc | false | <90% | 82028 | ||
NM_001002912 | C1orf173 | 4728 | 4746 | c | a | C | U | G | A | A | A | C | c | C | G | A | G | A | G | A | A | g | -1 | 4 | 8 | bc | false | <90% | 7165 | ||
NM_183380 | DST | 254 | 272 | U | G | C | U | G | A | A | A | C | c | C | G | A | G | A | G | g | g | A | -8 | 3 | 9 | c | false | <90% | 18036 | ||
NM_003089 | SNRP70 | 616 | 634 | U | G | C | U | G | A | A | A | C | c | C | G | A | G | A | G | g | A | g | -11 | 3 | 9 | c | false | <90% | 1940 | ||
NM_002077 | GOLGA1 | 1162 | 1180 | U | G | C | U | G | A | A | A | C | u | C | a | A | G | A | G | A | A | A | -16 | 2 | 9 | false | <90% | 4805 | |||
XR_017088 | LOC441774 | 737 | 755 | U | G | C | U | G | A | A | A | a | G | a | G | A | G | A | G | A | A | g | -26 | 3 | 8 | c | false | <90% | 803 | ||
XR_018247 | LOC441774 | 737 | 755 | U | G | C | U | G | A | A | A | a | G | a | G | A | G | A | G | A | A | g | -26 | 3 | 8 | c | false | <90% | 803 | ||
NM_002055 | GFAP | 2403 | 2421 | U | G | C | U | G | A | A | A | C | a | g | G | A | G | A | G | A | A | A | -44 | 2 | 9 | c | false | <90% | 3035 | ||
NM_001160 | APAF1 | 2473 | 2491 | a | G | C | U | G | A | A | A | C | a | g | G | A | G | A | G | A | A | A | -46 | 3 | 8 | c | false | <90% | 7042 | ||
NM_181868 | APAF1 | 2506 | 2524 | a | G | C | U | G | A | A | A | C | a | g | G | A | G | A | G | A | A | A | -46 | 3 | 8 | c | false | <90% | 7075 | ||
NM_013229 | APAF1 | 2473 | 2491 | a | G | C | U | G | A | A | A | C | a | g | G | A | G | A | G | A | A | A | -46 | 3 | 8 | c | false | <90% | 7171 | ||
NM_181861 | APAF1 | 2506 | 2524 | a | G | C | U | G | A | A | A | C | a | g | G | A | G | A | G | A | A | A | -46 | 3 | 8 | c | false | <90% | 7204 |
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_033129 | SCRT2 | 1870 | 1888 | U | U | U | C | U | C | U | C | G | C | u | U | c | U | C | A | G | C | u | 23 | 3 | 10 | false | <90% | 3599 | |||
NM_153742 | CTH | 129 | 147 | c | U | U | C | U | u | U | C | G | C | G | g | U | U | C | A | G | C | A | 0 | 3 | 7 | false | <90% | 1687 | |||
NM_001902 | CTH | 129 | 147 | c | U | U | C | U | u | U | C | G | C | G | g | U | U | C | A | G | C | A | 0 | 3 | 7 | false | <90% | 1819 | |||
XM_001132788 | LOC730170 | 234 | 252 | U | c | c | C | U | C | U | C | G | g | G | U | U | U | C | A | G | C | A | -13 | 3 | 9 | bc | false | <90% | 627 | ||
NM_012331 | MSRA | 1372 | 1390 | U | U | U | C | U | C | U | C | c | C | u | U | U | U | C | A | G | C | c | -26 | 3 | 8 | c | false | <90% | 1502 |
3 prime UTR Seed matches
Hits to same gene : 0
Hits to other genes : 3043
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