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mmu_circAp3d1_334
Basic information of circular RNA
PanCircBase ID:
mmu_circAp3d1_334
mm39_Chr. Position ID:
chr10|80547945|80548764|-
Gene name:
Ap3d1
Transcript:
ENSMUST00000020420.9
CircRNA type:
Exonic circular (circ)RNA
Exon/Intron count:
3
Exon/intron indexes:
23,22,21
Exon/intron offsets:
0,484,653
Genomic length:
819
Exon/intron sizes in nt:
96,72,166
Flanking exon/introns:
chr10:80546666-80547945|chr10:80548764-80549390
Splice length:
334
Other database IDs:
circAtlas: mmu-Ap3d1_0024
Human Ortholog IDs:
Mature spliced Sequence:
ACCCCTGGCTGACAGTGAGAAGCTGCCTGTCCAGAAACATAGAAATGCGGAGGCGGTGAAGTCCCCAGAGAAGGAGGGTGTGCTCGGGGTAGAGAAGAAGAGCAAGAAGCCCAAGAAGAAGGAGAAGAAGACCAAAGAGAGAGAGAGAGAGAAGAAGGACAAGAAGGGTGAGGACTTAGACTTCTGGCTGTCCACCACCCCACCACCTGCTGCTGCCCCCATTCCTGCCCCGTCCACGGAAGAACTTGCTGCAAGCACTATCACCTCCCCTAAGGATGAGTGTGAGGTTCTCAAAGGGGAAGAGGAGGACCACGTGGATCATGACCAAGAAAGG
Divergent primers for circular RNA PCR
Primer Set-1
Forward primer
Tm
Reverse primer
Tm
Product size
AAAGGGGAAGAGGAGGACCA
59.8
TCTTCTCTACCCCGAGCACA
59.96
140
Primer Set-2
Forward primer
Tm
Reverse primer
Tm
Product size
TGCAAGCACTATCACCTCCC
59.75
CTTCTCTGGGGACTTCACCG
59.75
158
PCR template sequence:
CACGGAAGAACTTGCTGCAAGCACTATCACCTCCCCTAAGGATGAGTGTGAGGTTCTCAAAGGGGAAGAGGAGGACCACGTGGATCATGACCAAGAAAGGACCCCTGGCTGACAGTGAGAAGCTGCCTGTCCAGAAACATAGAAATGCGGAGGCGGTGAAGTCCCCAGAGAAGGAGGGTGTGCTCGGGGTAGAGAAGAAG
Note: Users can design additional primers for provided template sequence using Primer3 or NCBI primer-blast.
miRNAs associated with circular RNAs
No of miRNAs
4
Interacting miRNAs (#binding sites)
mmu-miR-9-5p(1), mmu-miR-15a-5p(1), mmu-miR-326-3p(1), mmu-miR-207(1)
siRNAs for circular RNA silencing
Junction sequence
TGACCAAGAAAGGACCCCTGGCTGAC
siRNA sets
TCAGCCAGGGGTCCTTTCT
Protein-coding potential of circular RNAs
CPAT analysis
CPAT ORF ID
CPAT Fickett
CPAT Hexamer
Coding probabilty
ORF length
CIRCAP3D1_334_ORF_1
1.1878
0.467900335
0.845431524
393
ORF sequence:
ATGAGTGTGAGGTTCTCAAAGGGGAAGAGGAGGACCACGTGGATCATGACCAAGAAAGGACCCCTGGCTGACAGTGAGAAGCTGCCTGTCCAGAAACATAGAAATGCGGAGGCGGTGAAGTCCCCAGAGAAGGAGGGTGTGCTCGGGGTAGAGAAGAAGAGCAAGAAGCCCAAGAAGAAGGAGAAGAAGACCAAAGAGAGAGAGAGAGAGAAGAAGGACAAGAAGGGTGAGGACTTAGACTTCTGGCTGTCCACCACCCCACCACCTGCTGCTGCCCCCATTCCTGCCCCGTCCACGGAAGAACTTGCTGCAAGCACTATCACCTCCCCTAAGGATGAGTGTGAGGTTCTCAAAGGGGAAGAGGAGGACCACGTGGATCATGACCAAGAAAGG
Peptide sequence:
MSVRFSKGKRRTTWIMTKKGPLADSEKLPVQKHRNAEAVKSPEKEGVLGVEKKSKKPKKKEKKTKEREREKKDKKGEDLDFWLSTTPPPAAAPIPAPSTEELAASTITSPKDECEVLKGEEEDHVDHDQER
IRESfinder result
IRESfinder score
0.243075717
IRES/non IRES
non-IRES
riboCIRC information
riboCIRC ID
NA
NA
Evidence
Peptide sequence:
NA
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