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mmu_circCux1_533
Basic information of circular RNA
PanCircBase ID:
mmu_circCux1_533
mm39_Chr. Position ID:
chr5|136388855|136436881|-
Gene name:
Cux1
Transcript:
ENSMUST00000176216.9
CircRNA type:
Exonic circular (circ)RNA
Exon/Intron count:
6
Exon/intron indexes:
8,7,6,5,4,3
Exon/intron offsets:
0,3257,10116,13320,32313,47978
Genomic length:
48026
Exon/intron sizes in nt:
67,77,124,138,79,48
Flanking exon/introns:
chr5:136368991-136388855|chr5:136436881-136514594
Splice length:
533
Other database IDs:
circAtlas: mmu-Cux1_0003
circAtlas: hsa-SCAF8_0001, CIRCpedia: HSA_CIRCpedia_346027
Human Ortholog IDs:
Mature spliced Sequence:
GATTTACGCAAGCAGGTAGCACCACTGCTAAAGAGCTTCCAAGGGGAGATTGATGCACTGAGTAAAAGAAGCAAAGAAGCAGAGGCAGCCTTCTTGACTGTGTACAAGAGACTAATTGATGTTCCAGATCCGGTACCAGCCCTGGACGTCGGGCAACAGCTGGAAATAAAAGTGCAGCGTCTACACGACATTGAAACAGAGAACCAGAAACTTAGGGAAACACTAGAAGAGTACAACAAGGAGTTTGCTGAAGTGAAAAATCAAGAGGTTACGATAAAAGCACTTAAGGAGAAAATCCGAGAATACGAGCAGACCCTGAAGAGTCAGGCCGAGACCATTGCTCTGGAGAAAGAGCAGAAGCTACAAAATGATTTTGCAGAGAAGGAGAGAAAGCTGCAAGAGACACAGATGTCCACCACCTCAAAACTGGAGGAAGCTGAGCACAAACTCCAGACTCTGCAAACAGCCCTGGAAAAAACTCGAACAGAATTATTTGACCTGAAAACCAAATATGATGAAGAAACTACTGCAAA
Divergent primers for circular RNA PCR
Primer Set-1
Forward primer
Tm
Reverse primer
Tm
Product size
TCTGCAAACAGCCCTGGAAA
60.11
AAGGCTGCCTCTGCTTCTTT
59.89
170
Primer Set-2
Forward primer
Tm
Reverse primer
Tm
Product size
TCCAGACTCTGCAAACAGCC
60.25
AAGGCTGCCTCTGCTTCTTT
59.89
177
PCR template sequence:
AAGCTGAGCACAAACTCCAGACTCTGCAAACAGCCCTGGAAAAAACTCGAACAGAATTATTTGACCTGAAAACCAAATATGATGAAGAAACTACTGCAAAGATTTACGCAAGCAGGTAGCACCACTGCTAAAGAGCTTCCAAGGGGAGATTGATGCACTGAGTAAAAGAAGCAAAGAAGCAGAGGCAGCCTTCTTGACTG
Note: Users can design additional primers for provided template sequence using Primer3 or NCBI primer-blast.
miRNAs associated with circular RNAs
No of miRNAs
6
Interacting miRNAs (#binding sites)
mmu-miR-34c-5p(1), mmu-miR-148b-3p(1), mmu-miR-199b-3p(1), mmu-miR-199a-3p(1), mmu-miR-467b-5p(1), mmu-miR-1904(1)
siRNAs for circular RNA silencing
Junction sequence
AAACTACTGCAAAGATTTACGCAAGC
siRNA sets
TAAATCTTTGCAGTAGTTT
Protein-coding potential of circular RNAs
CPAT analysis
CPAT ORF ID
CPAT Fickett
CPAT Hexamer
Coding probabilty
ORF length
CIRCCUX1_533_ORF_1
0.7392
0.217523655
0.122937797
144
ORF sequence:
ATGTCCACCACCTCAAAACTGGAGGAAGCTGAGCACAAACTCCAGACTCTGCAAACAGCCCTGGAAAAAACTCGAACAGAATTATTTGACCTGAAAACCAAATATGATGAAGAAACTACTGCAAAGATTTACGCAAGCAGGTAG
Peptide sequence:
MSTTSKLEEAEHKLQTLQTALEKTRTELFDLKTKYDEETTAKIYASR
IRESfinder result
IRESfinder score
0.456439585
IRES/non IRES
non-IRES
riboCIRC information
riboCIRC ID
NA
NA
Evidence
Peptide sequence:
NA
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