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mmu_circCux2_313
Basic information of circular RNA
PanCircBase ID:
mmu_circCux2_313
mm39_Chr. Position ID:
chr5|122036339|122181907|-
Gene name:
Cux2
Transcript:
ENSMUST00000111752.10
CircRNA type:
Exonic circular (circ)RNA
Exon/Intron count:
4
Exon/intron indexes:
5,4,3,2
Exon/intron offsets:
0,23037,26528,145493
Genomic length:
145568
Exon/intron sizes in nt:
79,48,111,75
Flanking exon/introns:
chr5:122025551-122036339|chr5:122181907-122187838
Splice length:
313
Other database IDs:
CIRCpedia: MMU_CIRCpedia_5639, circAtlas: mmu-Cux2_0006
Human Ortholog IDs:
Mature spliced Sequence:
TGGGACTGTTAGTATTCTCCTACTACACGGAGTACGGCGGTGTTCAGCAGAGCGTGGGGCGTGCGATCATGCTTTAAGGAGCTTAGTTCTGTCGCCTCGGAGCTGTCTGCGCCACAGGAGGAAAGCGGACTTTCTCCTAAACATTTCATTGAACTCCGCCGGGAATTTAAGAAAGATGTGCCAGAGGGAATCAGAGCGATGGTAGCTCCGGTGCTGAAGAGCTTCCAGGCTGAGGTGGTGGCTCTCAGTAAAAGAAGTCGGGAGGCAGAGGCGGCGTTCCTGAGTGTTTATAAGCAATTGATTGAAGCACCAG
Divergent primers for circular RNA PCR
Primer Set-1
Forward primer
Tm
Reverse primer
Tm
Product size
GAAGAGCTTCCAGGCTGAGG
60.11
TTAAAGCATGATCGCACGCC
59.62
175
Primer Set-2
Forward primer
Tm
Reverse primer
Tm
Product size
TGAGGTGGTGGCTCTCAGTA
59.89
TTAAAGCATGATCGCACGCC
59.62
160
PCR template sequence:
CTGAAGAGCTTCCAGGCTGAGGTGGTGGCTCTCAGTAAAAGAAGTCGGGAGGCAGAGGCGGCGTTCCTGAGTGTTTATAAGCAATTGATTGAAGCACCAGTGGGACTGTTAGTATTCTCCTACTACACGGAGTACGGCGGTGTTCAGCAGAGCGTGGGGCGTGCGATCATGCTTTAAGGAGCTTAGTTCTGTCGCCTCGG
Note: Users can design additional primers for provided template sequence using Primer3 or NCBI primer-blast.
miRNAs associated with circular RNAs
No of miRNAs
2
Interacting miRNAs (#binding sites)
mmu-miR-137-3p(1), mmu-miR-203-3p(1)
siRNAs for circular RNA silencing
Junction sequence
ATTGAAGCACCAGTGGGACTGTTAGT
siRNA sets
NA
Protein-coding potential of circular RNAs
CPAT analysis
CPAT ORF ID
CPAT Fickett
CPAT Hexamer
Coding probabilty
ORF length
CIRCCUX2_313_ORF_1
1.049
0.232104441
0.274387261
192
ORF sequence:
ATGGTAGCTCCGGTGCTGAAGAGCTTCCAGGCTGAGGTGGTGGCTCTCAGTAAAAGAAGTCGGGAGGCAGAGGCGGCGTTCCTGAGTGTTTATAAGCAATTGATTGAAGCACCAGTGGGACTGTTAGTATTCTCCTACTACACGGAGTACGGCGGTGTTCAGCAGAGCGTGGGGCGTGCGATCATGCTTTAA
Peptide sequence:
MVAPVLKSFQAEVVALSKRSREAEAAFLSVYKQLIEAPVGLLVFSYYTEYGGVQQSVGRAIML
IRESfinder result
IRESfinder score
0.422293442
IRES/non IRES
non-IRES
riboCIRC information
riboCIRC ID
NA
NA
Evidence
Peptide sequence:
NA
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