Automatic recommendation
OK - siRNA is specific for both sense and antisense (guide) strands
43 hits were found for CUCACUCGUGAGCUCAAUG (2 guide strand hits and 41 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_173362 | RFESD | 629 | 647 | C | U | C | A | C | U | C | G | U | G | A | u | C | a | C | A | A | U | u | 41 | 3 | 11 | false | <90% | 2711 | |||
NM_017850 | C1orf109 | 1901 | 1919 | C | U | C | A | C | U | C | c | U | G | A | G | C | U | C | A | A | g | G | 35 | 2 | 9 | c | false | <90% | 2376 |
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_014593 | CXXC1 | 1945 | 1963 | C | u | U | U | G | A | G | C | U | C | A | C | G | g | G | U | G | A | c | 64 | 3 | 11 | c | false | <90% | 2444 | ||
NM_001037969 | ALAS2 | 1546 | 1564 | C | u | U | U | G | A | G | C | U | C | A | u | G | A | G | U | G | A | G | 54 | 2 | 9 | false | <90% | 1745 | |||
NM_001037967 | ALAS2 | 1631 | 1649 | C | u | U | U | G | A | G | C | U | C | A | u | G | A | G | U | G | A | G | 54 | 2 | 9 | false | <90% | 1830 | |||
NM_001037968 | ALAS2 | 1738 | 1756 | C | u | U | U | G | A | G | C | U | C | A | u | G | A | G | U | G | A | G | 54 | 2 | 9 | false | <90% | 1937 | |||
NM_000032 | ALAS2 | 1742 | 1760 | C | u | U | U | G | A | G | C | U | C | A | u | G | A | G | U | G | A | G | 54 | 2 | 9 | false | <90% | 1941 | |||
NM_000110 | DPYD | 1966 | 1984 | u | A | U | U | G | A | G | C | U | C | A | u | c | A | G | U | G | A | G | 53 | 3 | 10 | false | <90% | 4451 | |||
NM_001011649 | CDK5RAP2 | 1728 | 1746 | u | c | U | U | G | A | G | C | U | C | A | g | G | A | G | U | G | A | a | 47 | 4 | 9 | false | <90% | 5993 | |||
NM_018249 | CDK5RAP2 | 1728 | 1746 | u | c | U | U | G | A | G | C | U | C | A | g | G | A | G | U | G | A | a | 47 | 4 | 9 | false | <90% | 6230 | |||
NM_007047 | BTN3A2 | 1369 | 1387 | C | A | U | U | u | A | G | C | U | C | A | C | G | A | G | U | G | g | u | 40 | 3 | 12 | c | false | <90% | 3812 | ||
NM_022490 | POLR1E | 1513 | 1531 | C | A | U | U | G | A | G | C | U | C | A | g | G | A | G | U | u | u | G | 40 | 3 | 11 | false | <90% | 1854 | |||
XM_373056 | LOC391742 | 88 | 106 | a | g | g | U | G | A | G | C | U | C | A | g | G | A | G | U | G | A | G | 33 | 4 | 8 | false | <90% | 552 | |||
XM_941127 | LOC391742 | 88 | 106 | a | g | g | U | G | A | G | C | U | C | A | g | G | A | G | U | G | A | G | 33 | 4 | 8 | false | <90% | 552 | |||
XM_373078 | LOC391767 | 133 | 151 | a | u | g | U | G | A | G | C | U | C | A | g | G | A | G | U | G | A | G | 33 | 4 | 8 | false | <90% | 594 | |||
XM_936313 | LOC391767 | 133 | 151 | a | u | g | U | G | A | G | C | U | C | A | g | G | A | G | U | G | A | G | 33 | 4 | 8 | false | <90% | 594 | |||
XM_377879 | LOC646103 | 133 | 151 | a | g | g | U | G | A | G | C | U | C | A | g | G | A | G | U | G | A | G | 33 | 4 | 8 | false | <90% | 597 | |||
XM_373058 | LOC391746 | 133 | 151 | a | g | g | U | G | A | G | C | U | C | A | g | G | A | G | U | G | A | G | 33 | 4 | 8 | false | <90% | 597 | |||
XM_116384 | LOC646066 | 133 | 151 | a | g | g | U | G | A | G | C | U | C | A | g | G | A | G | U | G | A | G | 33 | 4 | 8 | false | <90% | 597 | |||
XM_373059 | LOC391747 | 133 | 151 | a | g | g | U | G | A | G | C | U | C | A | g | G | A | G | U | G | A | G | 33 | 4 | 8 | false | <90% | 597 | |||
XM_377875 | LOC402199 | 133 | 151 | a | g | g | U | G | A | G | C | U | C | A | g | G | A | G | U | G | A | G | 33 | 4 | 8 | false | <90% | 597 | |||
XM_373061 | LOC391749 | 133 | 151 | a | g | g | U | G | A | G | C | U | C | A | g | G | A | G | U | G | A | G | 33 | 4 | 8 | false | <90% | 597 | |||
XM_210613 | LOC285563 | 133 | 151 | a | g | g | U | G | A | G | C | U | C | A | g | G | A | G | U | G | A | G | 33 | 4 | 8 | false | <90% | 597 | |||
XM_001131061 | LOC729694 | 133 | 151 | a | g | g | U | G | A | G | C | U | C | A | g | G | A | G | U | G | A | G | 33 | 4 | 8 | false | <90% | 597 | |||
XM_001131065 | LOC729695 | 133 | 151 | a | g | g | U | G | A | G | C | U | C | A | g | G | A | G | U | G | A | G | 33 | 4 | 8 | false | <90% | 597 | |||
XM_001131072 | LOC729698 | 133 | 151 | a | g | g | U | G | A | G | C | U | C | A | g | G | A | G | U | G | A | G | 33 | 4 | 8 | false | <90% | 597 | |||
XM_001131081 | LOC729700 | 133 | 151 | a | g | g | U | G | A | G | C | U | C | A | g | G | A | G | U | G | A | G | 33 | 4 | 8 | false | <90% | 597 | |||
XM_001131089 | LOC729703 | 133 | 151 | a | g | g | U | G | A | G | C | U | C | A | g | G | A | G | U | G | A | G | 33 | 4 | 8 | false | <90% | 597 | |||
XM_001131091 | LOC729706 | 133 | 151 | a | g | g | U | G | A | G | C | U | C | A | g | G | A | G | U | G | A | G | 33 | 4 | 8 | false | <90% | 597 | |||
XM_001131099 | LOC729711 | 133 | 151 | a | g | g | U | G | A | G | C | U | C | A | g | G | A | G | U | G | A | G | 33 | 4 | 8 | false | <90% | 597 | |||
XM_377884 | LOC402207 | 133 | 151 | a | g | g | U | G | A | G | C | U | C | A | g | G | A | G | U | G | A | G | 33 | 4 | 8 | false | <90% | 597 | |||
XM_001131122 | LOC729719 | 133 | 151 | a | g | g | U | G | A | G | C | U | C | A | g | G | A | G | U | G | A | G | 33 | 4 | 8 | false | <90% | 597 | |||
XM_001131132 | LOC729724 | 133 | 151 | a | g | g | U | G | A | G | C | U | C | A | g | G | A | G | U | G | A | G | 33 | 4 | 8 | false | <90% | 597 | |||
XM_001131140 | LOC729731 | 133 | 151 | a | g | g | U | G | A | G | C | U | C | A | g | G | A | G | U | G | A | G | 33 | 4 | 8 | false | <90% | 597 | |||
XM_373073 | LOC391761 | 133 | 151 | a | g | g | U | G | A | G | C | U | C | A | g | G | A | G | U | G | A | G | 33 | 4 | 8 | false | <90% | 597 | |||
XM_001131155 | LOC729735 | 133 | 151 | a | g | g | U | G | A | G | C | U | C | A | g | G | A | G | U | G | A | G | 33 | 4 | 8 | false | <90% | 597 | |||
XM_373075 | LOC391763 | 133 | 151 | a | g | g | U | G | A | G | C | U | C | A | g | G | A | G | U | G | A | G | 33 | 4 | 8 | false | <90% | 597 | |||
XM_373077 | LOC391766 | 133 | 151 | a | g | g | U | G | A | G | C | U | C | A | g | G | A | G | U | G | A | G | 33 | 4 | 8 | false | <90% | 597 | |||
XM_936249 | LOC202201 | 133 | 151 | a | g | g | U | G | A | G | C | U | C | A | g | G | A | G | U | G | A | G | 33 | 4 | 8 | false | <90% | 597 | |||
XM_936303 | LOC391766 | 133 | 151 | a | g | g | U | G | A | G | C | U | C | A | g | G | A | G | U | G | A | G | 33 | 4 | 8 | false | <90% | 597 | |||
NM_006908 | RAC1 | 1310 | 1328 | C | A | U | U | G | A | a | C | U | C | A | C | c | A | G | U | G | A | G | 23 | 2 | 6 | false | <90% | 2355 | |||
NM_018890 | RAC1 | 1367 | 1385 | C | A | U | U | G | A | a | C | U | C | A | C | c | A | G | U | G | A | G | 23 | 2 | 6 | false | <90% | 2412 | |||
NM_198829 | RAC1 | 1368 | 1386 | C | A | U | U | G | A | a | C | U | C | A | C | c | A | G | U | G | A | G | 23 | 2 | 6 | false | <90% | 2413 |
3 prime UTR Seed matches
Hits to same gene : 0
Hits to other genes : 2469
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