Automatic recommendation
OK - siRNA is specific for both sense and antisense (guide) strands
59 hits were found for CCUCUCCUCUUCCAUAGGC (34 guide strand hits and 25 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_001626 | AKT2 | 4345 | 4363 | u | C | U | C | U | C | C | U | C | U | U | C | C | A | c | A | G | G | a | 68 | 3 | 13 | c | false | <90% | 5263 | ||
NM_015425 | POLR1A | 647 | 665 | C | C | U | C | U | C | C | U | C | U | U | C | g | A | U | A | a | G | C | 66 | 2 | 12 | false | <90% | 6637 | |||
NM_001080452 | GPR108 | 962 | 980 | u | C | U | C | U | C | C | U | C | U | U | C | C | A | c | A | G | c | a | 65 | 4 | 13 | c | false | <90% | 2076 | ||
NM_020171 | GPR108 | 1100 | 1118 | u | C | U | C | U | C | C | U | C | U | U | C | C | A | c | A | G | c | a | 65 | 4 | 13 | c | false | <90% | 2214 | ||
NM_181483 | C18orf1 | 230 | 248 | a | C | U | C | U | C | C | U | C | U | U | C | C | A | U | g | G | c | a | 64 | 4 | 14 | c | false | <90% | 8031 | ||
NM_004338 | C18orf1 | 230 | 248 | a | C | U | C | U | C | C | U | C | U | U | C | C | A | U | g | G | c | a | 64 | 4 | 14 | c | false | <90% | 8085 | ||
NM_004637 | RAB7A | 927 | 945 | C | C | U | C | U | C | C | U | C | U | U | C | C | A | a | A | c | a | a | 44 | 4 | 14 | c | false | <90% | 2240 | ||
XM_001134334 | RBM19 | 1781 | 1799 | C | C | U | u | U | C | C | U | C | U | U | C | C | A | c | A | G | G | a | 33 | 3 | 10 | c | false | <90% | 4224 | ||
NM_006045 | ATP9A | 4108 | 4126 | a | C | U | C | U | u | C | U | C | U | U | C | C | A | U | A | G | a | a | 27 | 4 | 11 | c | false | <90% | 7580 | ||
XM_001130755 | LOC729602 | 932 | 950 | C | C | U | C | U | C | C | U | C | U | U | C | C | A | c | c | c | u | C | 23 | 4 | 14 | c | false | <90% | 1119 | ||
XM_001130755 | LOC729602 | 995 | 1013 | C | C | U | C | U | C | C | U | C | U | U | C | C | A | c | c | c | u | C | 23 | 4 | 14 | c | false | <90% | 1119 | ||
XM_370958 | LOC388237 | 692 | 710 | C | C | U | C | U | C | C | U | C | U | U | C | C | A | c | c | c | u | C | 23 | 4 | 14 | c | false | <90% | 1136 | ||
XM_370958 | LOC388237 | 755 | 773 | C | C | U | C | U | C | C | U | C | U | U | C | C | A | c | c | c | u | C | 23 | 4 | 14 | c | false | <90% | 1136 | ||
XM_001132759 | LOC728734 | 692 | 710 | C | C | U | C | U | C | C | U | C | U | U | C | C | A | c | c | c | u | C | 23 | 4 | 14 | c | false | <90% | 1156 | ||
XM_001132759 | LOC728734 | 755 | 773 | C | C | U | C | U | C | C | U | C | U | U | C | C | A | c | c | c | u | C | 23 | 4 | 14 | c | false | <90% | 1156 | ||
XM_001132759 | LOC728734 | 818 | 836 | C | C | U | C | U | C | C | U | C | U | U | C | C | A | c | c | c | u | C | 23 | 4 | 14 | c | false | <90% | 1156 | ||
XM_001132804 | LOC728741 | 692 | 710 | C | C | U | C | U | C | C | U | C | U | U | C | C | A | c | c | c | u | C | 23 | 4 | 14 | c | false | <90% | 1156 | ||
XM_001132804 | LOC728741 | 755 | 773 | C | C | U | C | U | C | C | U | C | U | U | C | C | A | c | c | c | u | C | 23 | 4 | 14 | c | false | <90% | 1156 | ||
XM_001132804 | LOC728741 | 818 | 836 | C | C | U | C | U | C | C | U | C | U | U | C | C | A | c | c | c | u | C | 23 | 4 | 14 | c | false | <90% | 1156 | ||
NM_001018059 | LOC440348 | 740 | 758 | C | C | U | C | U | C | C | U | C | U | U | C | C | A | c | c | c | u | C | 23 | 4 | 14 | c | false | <90% | 1184 | ||
NM_001018059 | LOC440348 | 803 | 821 | C | C | U | C | U | C | C | U | C | U | U | C | C | A | c | c | c | u | C | 23 | 4 | 14 | c | false | <90% | 1184 | ||
XM_001132675 | LOC730153 | 969 | 987 | C | C | U | C | U | C | C | U | C | U | U | C | C | A | c | c | c | u | C | 23 | 4 | 14 | c | false | <90% | 1240 | ||
XM_001132675 | LOC730153 | 1032 | 1050 | C | C | U | C | U | C | C | U | C | U | U | C | C | A | c | c | c | u | C | 23 | 4 | 14 | c | false | <90% | 1240 | ||
XM_001132675 | LOC730153 | 1095 | 1113 | C | C | U | C | U | C | C | U | C | U | U | C | C | A | c | c | c | u | C | 23 | 4 | 14 | c | false | <90% | 1240 | ||
NM_003053 | SLC18A1 | 171 | 189 | C | C | U | C | c | C | C | U | C | U | U | C | C | A | U | A | a | a | g | 17 | 4 | 11 | c | false | <90% | 2749 | ||
NM_001001712 | LCN10 | 519 | 537 | C | u | g | C | U | g | C | U | C | U | U | C | C | A | U | A | G | G | C | 5 | 3 | 13 | bc | false | <90% | 2047 | ||
NM_153189 | SPAM1 | 615 | 633 | C | C | U | C | U | u | C | U | C | U | U | u | C | A | U | A | G | G | a | -2 | 3 | 6 | false | <90% | 2009 | |||
NM_003117 | SPAM1 | 609 | 627 | C | C | U | C | U | u | C | U | C | U | U | u | C | A | U | A | G | G | a | -2 | 3 | 6 | false | <90% | 2395 | |||
XR_015959 | LOC729348 | 1317 | 1335 | C | C | U | C | U | C | C | U | C | c | U | C | C | A | a | A | G | G | a | -12 | 3 | 9 | c | false | <90% | 2271 | ||
XR_015993 | LOC731767 | 1317 | 1335 | C | C | U | C | U | C | C | U | C | c | U | C | C | A | a | A | G | G | a | -12 | 3 | 9 | c | false | <90% | 2271 | ||
XM_001131241 | LOC731914 | 2323 | 2341 | C | C | U | C | U | C | C | U | C | c | U | C | C | A | a | A | G | G | a | -12 | 3 | 9 | c | false | <90% | 2858 | ||
XR_015757 | LOC728678 | 2323 | 2341 | C | C | U | C | U | C | C | U | C | c | U | C | C | A | a | A | G | G | a | -12 | 3 | 9 | c | false | <90% | 3291 | ||
XR_017717 | LOC389651 | 1961 | 1979 | C | C | U | C | U | C | C | U | C | c | U | C | C | A | a | A | G | G | a | -12 | 3 | 9 | c | false | <90% | 3918 | ||
XR_015162 | LOC727880 | 1961 | 1979 | C | C | U | C | U | C | C | U | C | c | U | C | C | A | a | A | G | G | a | -12 | 3 | 9 | c | false | <90% | 3938 |
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_152688 | KHDRBS2 | 277 | 295 | c | g | C | U | A | U | G | G | A | A | G | A | G | G | A | G | A | a | a | 78 | 4 | 15 | ac | false | <90% | 2366 | ||
NM_178425 | HDAC9 | 3222 | 3240 | G | C | C | U | A | U | G | G | A | A | G | A | G | G | A | G | c | c | a | 68 | 3 | 16 | ac | false | <90% | 4559 | ||
NM_178423 | HDAC9 | 3322 | 3340 | G | C | C | U | A | U | G | G | A | A | G | A | G | G | A | G | c | c | a | 68 | 3 | 16 | ac | false | <90% | 4659 | ||
XR_015368 | LOC728735 | 2720 | 2738 | c | C | C | U | A | U | G | G | A | A | G | u | G | G | A | G | A | G | c | 59 | 3 | 10 | false | <90% | 4286 | |||
XR_017086 | LOC645954 | 325 | 343 | G | g | C | U | A | U | G | G | A | A | G | A | G | G | A | G | g | c | a | 57 | 4 | 14 | ac | false | <90% | 4019 | ||
NM_183075 | CYP2U1 | 1057 | 1075 | c | C | a | c | A | U | G | G | A | A | G | A | G | G | A | G | A | G | G | 41 | 3 | 15 | bc | false | <90% | 4760 | ||
NM_000779 | CYP4B1 | 598 | 616 | a | C | C | U | u | U | G | G | A | A | G | A | G | G | A | G | A | c | a | 38 | 4 | 12 | c | false | <90% | 2147 | ||
NM_000830 | GRIK1 | 211 | 229 | G | C | C | c | A | U | G | G | A | A | G | A | G | G | A | G | g | a | G | 37 | 3 | 12 | c | false | <90% | 3231 | ||
NM_175611 | GRIK1 | 211 | 229 | G | C | C | c | A | U | G | G | A | A | G | A | G | G | A | G | g | a | G | 37 | 3 | 12 | c | false | <90% | 3489 | ||
NM_006037 | HDAC4 | 4018 | 4036 | G | C | C | c | A | U | G | G | A | A | G | A | G | G | A | G | c | c | G | 37 | 3 | 12 | c | false | <90% | 8459 | ||
NM_024915 | GRHL2 | 1558 | 1576 | G | C | C | c | A | U | G | G | A | A | G | A | G | G | A | G | u | u | u | 32 | 4 | 12 | c | false | <90% | 4792 | ||
NM_175918 | CRIPAK | 1826 | 1844 | u | g | a | g | A | U | G | G | A | A | G | A | G | G | A | G | A | G | G | 30 | 4 | 15 | bc | false | <90% | 1935 | ||
NM_003772 | JRKL | 1167 | 1185 | c | C | C | U | A | U | G | G | u | A | G | A | G | G | A | G | A | a | a | 30 | 4 | 8 | c | false | <90% | 2930 | ||
XM_064152 | SRL | 426 | 444 | G | C | C | U | g | U | G | G | A | A | G | A | G | G | A | G | u | G | G | 25 | 2 | 11 | c | false | <90% | 5587 | ||
XM_942054 | SRL | 426 | 444 | G | C | C | U | g | U | G | G | A | A | G | A | G | G | A | G | u | G | G | 25 | 2 | 11 | c | false | <90% | 5587 | ||
XM_001127174 | LOC728319 | 713 | 731 | G | C | C | U | g | U | G | G | A | A | G | A | G | a | A | G | A | G | c | 24 | 3 | 8 | c | false | <90% | 942 | ||
XM_001127551 | LOC728487 | 743 | 761 | G | C | C | U | g | U | G | G | A | A | G | A | G | a | A | G | A | G | c | 24 | 3 | 8 | c | false | <90% | 972 | ||
XM_937233 | ANKRD36 | 743 | 761 | G | C | C | U | g | U | G | G | A | A | G | A | G | a | A | G | A | G | c | 24 | 3 | 8 | c | false | <90% | 987 | ||
NM_052909 | KIAA1909 | 7175 | 7193 | G | C | C | U | g | U | G | G | A | A | G | A | G | G | A | G | g | c | u | 17 | 4 | 11 | c | false | <90% | 11507 | ||
NM_004140 | LLGL1 | 3500 | 3518 | G | C | C | U | A | g | G | G | A | A | G | A | G | G | A | c | A | G | G | 10 | 2 | 9 | c | false | <90% | 4225 | ||
NM_032840 | SPRYD3 | 12 | 30 | G | C | C | U | A | U | G | G | A | u | G | A | G | G | A | G | g | a | c | -13 | 4 | 9 | c | false | <90% | 2568 | ||
XR_017486 | LOC401980 | 1104 | 1122 | G | C | C | U | g | a | G | G | A | A | G | A | G | G | A | G | A | G | a | -19 | 3 | 12 | bc | false | <90% | 1224 | ||
XR_015754 | LOC732184 | 1161 | 1179 | G | C | C | U | g | a | G | G | A | A | G | A | G | G | A | G | A | G | a | -19 | 3 | 12 | bc | false | <90% | 1281 | ||
NR_002836 | PGM5P2 | 1546 | 1564 | u | C | C | U | c | U | G | G | A | g | G | A | G | G | A | G | A | G | G | -36 | 3 | 9 | bc | false | <90% | 1988 | ||
NR_003133 | LOC400759 | 7326 | 7344 | u | C | C | U | u | U | G | G | A | g | G | A | G | G | A | G | A | G | G | -36 | 3 | 9 | bc | false | <90% | 16075 |
3 prime UTR Seed matches
Hits to same gene : 0
Hits to other genes : 4357
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