Automatic recommendation
Warning - siRNA is specific for only the antisense (guide) strand
31 hits were found for CAGAUUGCUGACUCCCAGC (24 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_001080973 | IL17RD | 309 | 327 | g | u | G | A | U | U | G | C | U | G | A | C | g | C | C | C | A | G | a | 71 | 4 | 10 | false | <90% | 8720 | |||
NM_017563 | IL17RD | 331 | 349 | g | u | G | A | U | U | G | C | U | G | A | C | g | C | C | C | A | G | a | 71 | 4 | 10 | false | <90% | 8742 | |||
NM_016173 | HEMK1 | 5570 | 5588 | C | A | G | A | U | U | G | C | U | G | A | C | c | u | C | C | A | G | a | 65 | 3 | 12 | false | <90% | 5862 | |||
NM_002031 | FRK | 2358 | 2376 | C | A | G | A | U | U | G | C | U | G | A | a | U | C | C | C | A | u | C | 63 | 2 | 11 | false | <90% | 2864 | |||
NM_000481 | AMT | 1823 | 1841 | a | u | G | A | U | U | G | C | U | G | A | C | U | C | a | C | A | G | u | 56 | 4 | 12 | c | false | <90% | 2117 | ||
NM_024837 | ATP8B4 | 3101 | 3119 | C | A | u | A | U | U | G | C | U | G | A | C | U | a | C | C | A | G | u | 55 | 3 | 10 | c | false | <90% | 5679 | ||
XR_015910 | LOC731702 | 160 | 178 | C | A | a | A | U | U | G | C | U | G | A | C | U | C | a | C | A | G | a | 50 | 3 | 11 | c | false | <90% | 1297 | ||
XR_017346 | LOC645257 | 160 | 178 | C | A | a | A | U | U | G | C | U | G | A | C | U | C | a | C | A | G | a | 50 | 3 | 11 | c | false | <90% | 1297 | ||
NM_004475 | FLOT2 | 754 | 772 | a | A | G | A | U | U | G | C | U | G | A | C | U | C | u | a | A | G | C | 47 | 3 | 13 | c | false | <90% | 2659 | ||
NM_024874 | KIAA0319L | 1045 | 1063 | C | A | G | A | U | U | G | C | U | G | u | C | c | C | C | C | A | G | C | 28 | 2 | 10 | false | <90% | 4804 | |||
NM_182686 | KIAA0319L | 1045 | 1063 | C | A | G | A | U | U | G | C | U | G | u | C | c | C | C | C | A | G | C | 28 | 2 | 10 | false | <90% | 5692 | |||
NM_024654 | NOL9 | 1288 | 1306 | C | c | G | A | U | U | G | C | U | G | u | C | U | C | C | C | A | G | C | 27 | 2 | 8 | c | false | <90% | 2837 | ||
NR_003370 | LOC730092 | 18580 | 18598 | C | A | G | A | U | U | G | C | U | G | c | C | U | g | C | C | A | G | C | 19 | 2 | 10 | c | false | <90% | 26557 | ||
NR_003095 | E2F6 | 1829 | 1847 | C | u | a | A | U | U | G | C | U | G | u | C | U | C | C | C | A | G | C | 7 | 3 | 8 | c | false | <90% | 3185 | ||
NM_198256 | E2F6 | 1884 | 1902 | C | u | a | A | U | U | G | C | U | G | u | C | U | C | C | C | A | G | C | 7 | 3 | 8 | c | false | <90% | 3240 | ||
NR_003092 | E2F6 | 1955 | 1973 | C | u | a | A | U | U | G | C | U | G | u | C | U | C | C | C | A | G | C | 7 | 3 | 8 | c | false | <90% | 3311 | ||
NR_003093 | E2F6 | 2017 | 2035 | C | u | a | A | U | U | G | C | U | G | u | C | U | C | C | C | A | G | C | 7 | 3 | 8 | c | false | <90% | 3373 | ||
NR_003094 | E2F6 | 2088 | 2106 | C | u | a | A | U | U | G | C | U | G | u | C | U | C | C | C | A | G | C | 7 | 3 | 8 | c | false | <90% | 3444 | ||
NM_007249 | KLF12 | 8101 | 8119 | C | A | G | A | U | U | c | C | U | G | A | C | U | C | u | C | A | G | u | 4 | 3 | 7 | c | false | <90% | 10923 | ||
NM_001079524 | PAICS | 1805 | 1823 | g | g | c | A | U | U | a | C | U | G | A | C | U | C | C | C | A | G | C | 0 | 4 | 12 | bc | false | <90% | 3329 | ||
NM_006452 | PAICS | 1826 | 1844 | g | g | c | A | U | U | a | C | U | G | A | C | U | C | C | C | A | G | C | 0 | 4 | 12 | bc | false | <90% | 3350 | ||
NM_001079525 | PAICS | 1826 | 1844 | g | g | c | A | U | U | a | C | U | G | A | C | U | C | C | C | A | G | C | 0 | 4 | 12 | bc | false | <90% | 3350 | ||
NM_144668 | WDR66 | 479 | 497 | C | A | G | A | U | U | a | C | U | G | A | u | U | C | C | C | A | G | u | -5 | 3 | 6 | false | <90% | 3768 | |||
NM_012265 | RHBDD3 | 115 | 133 | u | A | G | A | g | U | c | C | U | G | A | C | U | C | C | C | A | G | C | -19 | 3 | 12 | bc | false | <90% | 1738 |
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 | |||||||||||||
XM_001133420 | LOC728991 | 1436 | 1454 | G | C | U | G | G | G | A | G | U | C | A | G | g | A | A | U | C | c | u | 81 | 3 | 12 | false | <90% | 2143 | |||
NM_006037 | HDAC4 | 7197 | 7215 | G | C | U | G | G | G | A | G | U | C | A | G | C | A | A | g | C | g | a | 66 | 3 | 15 | c | false | <90% | 8459 | ||
NR_001552 | TTTY16 | 42 | 60 | G | C | U | G | G | G | A | G | U | C | A | G | a | A | A | U | u | g | a | 58 | 4 | 12 | false | <90% | 192 | |||
NM_174976 | ZDHHC22 | 1585 | 1603 | u | C | U | G | G | G | A | G | a | C | A | G | C | A | A | U | C | a | a | 30 | 4 | 8 | c | false | <90% | 3408 | ||
XM_943029 | LOC389043 | 480 | 498 | c | C | U | G | G | c | A | G | U | C | A | G | C | c | A | U | C | U | G | 15 | 3 | 7 | c | false | <90% | 1861 | ||
XM_374012 | LOC389043 | 480 | 498 | c | C | U | G | G | c | A | G | U | C | A | G | C | c | A | U | C | U | G | 15 | 3 | 7 | c | false | <90% | 1861 | ||
NM_001949 | E2F3 | 1842 | 1860 | G | C | U | G | G | G | A | a | a | C | A | G | C | A | A | U | C | U | u | -27 | 3 | 9 | bc | false | <90% | 4744 |
3 prime UTR Seed matches
Hits to same gene : 0
Hits to other genes : 1877
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