Automatic recommendation
Warning - siRNA is specific for only the antisense (guide) strand
37 hits were found for GUCUGUACAGCAUCUUGAG (6 guide strand hits and 31 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 | |||||||||||||
XM_929730 | LOC646780 | 140 | 158 | a | U | g | U | G | U | A | C | A | G | C | A | U | C | U | U | G | g | c | 70 | 4 | 14 | c | false | <90% | 657 | ||
XM_001126879 | LOC646780 | 140 | 158 | a | U | g | U | G | U | A | C | A | G | C | A | U | C | U | U | G | g | c | 70 | 4 | 14 | c | false | <90% | 657 | ||
NM_002637 | PHKA1 | 300 | 318 | a | U | g | U | G | U | A | C | A | G | C | A | U | C | U | U | G | g | c | 70 | 4 | 14 | c | false | <90% | 4214 | ||
NM_183397 | PXMP4 | 4752 | 4770 | c | U | C | U | G | U | A | C | A | G | C | A | g | g | U | U | G | A | G | 68 | 3 | 11 | false | <90% | 5528 | |||
NM_007238 | PXMP4 | 4951 | 4969 | c | U | C | U | G | U | A | C | A | G | C | A | g | g | U | U | G | A | G | 68 | 3 | 11 | false | <90% | 5727 | |||
NM_024875 | SYNPO2L | 3297 | 3315 | a | g | g | U | G | U | A | C | A | G | C | A | U | C | U | U | G | u | G | 64 | 4 | 14 | c | false | <90% | 3470 |
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_006833 | COPS6 | 715 | 733 | a | U | C | A | A | G | A | U | G | C | U | G | c | A | C | A | G | c | C | 84 | 3 | 11 | false | <90% | 1441 | |||
XM_001132326 | LOC732232 | 427 | 445 | a | U | g | A | A | G | A | U | G | C | U | G | g | A | C | A | G | A | C | 68 | 3 | 9 | false | <90% | 1063 | |||
XM_001130017 | LOC729352 | 427 | 445 | a | U | g | A | A | G | A | U | G | C | U | G | g | A | C | A | G | A | C | 68 | 3 | 9 | false | <90% | 1063 | |||
XR_019244 | LOC389120 | 1897 | 1915 | C | c | a | A | A | G | A | U | G | C | U | G | g | A | C | A | G | A | C | 58 | 3 | 9 | false | <90% | 3571 | |||
XR_017199 | LOC389120 | 1897 | 1915 | C | c | a | A | A | G | A | U | G | C | U | G | g | A | C | A | G | A | C | 58 | 3 | 9 | false | <90% | 3571 | |||
NM_001001580 | PDE9A | 1485 | 1503 | u | U | C | A | u | G | A | U | G | C | U | G | U | A | C | A | G | A | a | 41 | 3 | 13 | bc | false | <90% | 1590 | ||
NM_001001576 | PDE9A | 1529 | 1547 | u | U | C | A | u | G | A | U | G | C | U | G | U | A | C | A | G | A | a | 41 | 3 | 13 | bc | false | <90% | 1634 | ||
NM_001001575 | PDE9A | 1570 | 1588 | u | U | C | A | u | G | A | U | G | C | U | G | U | A | C | A | G | A | a | 41 | 3 | 13 | bc | false | <90% | 1675 | ||
NM_001001569 | PDE9A | 1614 | 1632 | u | U | C | A | u | G | A | U | G | C | U | G | U | A | C | A | G | A | a | 41 | 3 | 13 | bc | false | <90% | 1719 | ||
NM_001001572 | PDE9A | 1625 | 1643 | u | U | C | A | u | G | A | U | G | C | U | G | U | A | C | A | G | A | a | 41 | 3 | 13 | bc | false | <90% | 1730 | ||
NM_001001577 | PDE9A | 1648 | 1666 | u | U | C | A | u | G | A | U | G | C | U | G | U | A | C | A | G | A | a | 41 | 3 | 13 | bc | false | <90% | 1753 | ||
NM_001001568 | PDE9A | 1669 | 1687 | u | U | C | A | u | G | A | U | G | C | U | G | U | A | C | A | G | A | a | 41 | 3 | 13 | bc | false | <90% | 1774 | ||
NM_001001579 | PDE9A | 1685 | 1703 | u | U | C | A | u | G | A | U | G | C | U | G | U | A | C | A | G | A | a | 41 | 3 | 13 | bc | false | <90% | 1790 | ||
NM_001001578 | PDE9A | 1692 | 1710 | u | U | C | A | u | G | A | U | G | C | U | G | U | A | C | A | G | A | a | 41 | 3 | 13 | bc | false | <90% | 1797 | ||
NM_001001574 | PDE9A | 1740 | 1758 | u | U | C | A | u | G | A | U | G | C | U | G | U | A | C | A | G | A | a | 41 | 3 | 13 | bc | false | <90% | 1845 | ||
NM_001001571 | PDE9A | 1747 | 1765 | u | U | C | A | u | G | A | U | G | C | U | G | U | A | C | A | G | A | a | 41 | 3 | 13 | bc | false | <90% | 1852 | ||
NM_001001584 | PDE9A | 1747 | 1765 | u | U | C | A | u | G | A | U | G | C | U | G | U | A | C | A | G | A | a | 41 | 3 | 13 | bc | false | <90% | 1852 | ||
NM_001001573 | PDE9A | 1805 | 1823 | u | U | C | A | u | G | A | U | G | C | U | G | U | A | C | A | G | A | a | 41 | 3 | 13 | bc | false | <90% | 1910 | ||
NM_001001567 | PDE9A | 1818 | 1836 | u | U | C | A | u | G | A | U | G | C | U | G | U | A | C | A | G | A | a | 41 | 3 | 13 | bc | false | <90% | 1923 | ||
NM_001001570 | PDE9A | 1839 | 1857 | u | U | C | A | u | G | A | U | G | C | U | G | U | A | C | A | G | A | a | 41 | 3 | 13 | bc | false | <90% | 1944 | ||
NM_001001581 | PDE9A | 1849 | 1867 | u | U | C | A | u | G | A | U | G | C | U | G | U | A | C | A | G | A | a | 41 | 3 | 13 | bc | false | <90% | 1954 | ||
NM_001001585 | PDE9A | 1872 | 1890 | u | U | C | A | u | G | A | U | G | C | U | G | U | A | C | A | G | A | a | 41 | 3 | 13 | bc | false | <90% | 1977 | ||
NM_001001583 | PDE9A | 1920 | 1938 | u | U | C | A | u | G | A | U | G | C | U | G | U | A | C | A | G | A | a | 41 | 3 | 13 | bc | false | <90% | 2025 | ||
NM_001001582 | PDE9A | 1927 | 1945 | u | U | C | A | u | G | A | U | G | C | U | G | U | A | C | A | G | A | a | 41 | 3 | 13 | bc | false | <90% | 2032 | ||
NM_002606 | PDE9A | 1998 | 2016 | u | U | C | A | u | G | A | U | G | C | U | G | U | A | C | A | G | A | a | 41 | 3 | 13 | bc | false | <90% | 2103 | ||
NM_001009922 | RCHY1 | 1705 | 1723 | u | U | C | u | A | G | A | U | G | C | U | G | U | A | g | A | G | A | C | 36 | 3 | 10 | c | false | <90% | 4309 | ||
NM_001008925 | RCHY1 | 1730 | 1748 | u | U | C | u | A | G | A | U | G | C | U | G | U | A | g | A | G | A | C | 36 | 3 | 10 | c | false | <90% | 4334 | ||
NM_015436 | RCHY1 | 1732 | 1750 | u | U | C | u | A | G | A | U | G | C | U | G | U | A | g | A | G | A | C | 36 | 3 | 10 | c | false | <90% | 4336 | ||
NM_000539 | RHO | 1766 | 1784 | a | g | C | A | A | G | A | a | G | C | U | G | U | A | C | A | G | A | u | 19 | 4 | 10 | bc | false | <90% | 2767 | ||
NM_032808 | LINGO1 | 757 | 775 | u | U | C | A | A | G | A | g | G | C | U | G | U | A | C | c | G | A | C | 9 | 3 | 7 | c | false | <90% | 2932 | ||
NM_001042475 | C6orf204 | 2147 | 2165 | C | U | C | u | A | G | A | U | G | a | U | G | U | A | C | A | G | A | g | -24 | 3 | 8 | bc | false | <90% | 3335 |
3 prime UTR Seed matches
Hits to same gene : 0
Hits to other genes : 1915
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