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mmu_circAtp2c1_435

Basic information of circular RNA
PanCircBase ID:

mmu_circAtp2c1_435

mm39_Chr. Position ID:

chr9|105322416|105330042|-

Gene name:

Atp2c1

Transcript:

ENSMUST00000177293.8

CircRNA type:

Exonic circular (circ)RNA

Exon/Intron count:

5

Exon/intron indexes:

8,7,6,5,4

Exon/intron offsets:

0,834,3604,6586,7557

Genomic length:

7626

Exon/intron sizes in nt:

98,125,67,76,69

Flanking exon/introns:

chr9:105320240-105322416|chr9:105330042-105330732

Splice length:

435

Other database IDs:

​

​

Human Ortholog IDs:
Mature spliced Sequence:

GGTATTGTCATTGGAACAGGAGAAAATTCTGAATTTGGAGAGGTCTTTAAGATGATGCAGGCAGAAGAAGCACCAAAAACTCCTCTGCAGAAGAGCATGGACCTCTTAGGCAAGCAGCTGTCCTTTTACTCCTTTGGTATAATAGGTATCATCATGTTGGTTGGCTGGTTACTAGGAAAAGACATTCTGGAAATGTTCACTATTAGTGTAAGCTTGGCTGTAGCTGCAATTCCTGAAGGCCTGCCTATTGTGGTCACGGTGACTCTAGCCCTTGGTGTTATGAGAATGGTGAAGAAAAGGGCTATTGTAAAGAAATTGCCTATTGTGGAAACACTGGGCTGCTGTAATGTGATTTGTTCAGATAAAACTGGAACCCTGACGAAGAACGAGATGACTGTTACTCACATCCTCACTTCCGATGGCCTGCATGCTGAG

Divergent primers for circular RNA PCR

Primer Set-1

Forward primer
Tm
Reverse primer
Tm
Product size

ACTGGAACCCTGACGAAGAAC

59.93

TGCTTCTTCTGCCTGCATCA

59.96

141

Primer Set-2

Forward primer
Tm
Reverse primer
Tm
Product size

GGAACCCTGACGAAGAACGA

59.68

GGTGCTTCTTCTGCCTGCAT

60.96

140

PCR template sequence:

GGGCTGCTGTAATGTGATTTGTTCAGATAAAACTGGAACCCTGACGAAGAACGAGATGACTGTTACTCACATCCTCACTTCCGATGGCCTGCATGCTGAGGGTATTGTCATTGGAACAGGAGAAAATTCTGAATTTGGAGAGGTCTTTAAGATGATGCAGGCAGAAGAAGCACCAAAAACTCCTCTGCAGAAGAGCATGG

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-199a-5p(1), mmu-miR-298-5p(1), mmu-miR-194-5p(1), mmu-miR-384-3p(1), mmu-miR-323-3p(1), mmu-miR-7a-1-3p(1)

siRNAs for circular RNA silencing
Junction sequence

CCTGCATGCTGAGGGTATTGTCATTG

siRNA sets

CAATGACAATACCCTCAGC,AATGACAATACCCTCAGCA,GACAATACCCTCAGCATGC

Protein-coding potential of circular RNAs

CPAT analysis

CPAT ORF ID
CPAT Fickett
CPAT Hexamer
Coding probabilty
ORF length

CIRCATP2C1_435_ORF_1

1.1656

0.151837251

0.968784702

819

ORF sequence:

ATGATGCAGGCAGAAGAAGCACCAAAAACTCCTCTGCAGAAGAGCATGGACCTCTTAGGCAAGCAGCTGTCCTTTTACTCCTTTGGTATAATAGGTATCATCATGTTGGTTGGCTGGTTACTAGGAAAAGACATTCTGGAAATGTTCACTATTAGTGTAAGCTTGGCTGTAGCTGCAATTCCTGAAGGCCTGCCTATTGTGGTCACGGTGACTCTAGCCCTTGGTGTTATGAGAATGGTGAAGAAAAGGGCTATTGTAAAGAAATTGCCTATTGTGGAAACACTGGGCTGCTGTAATGTGATTTGTTCAGATAAAACTGGAACCCTGACGAAGAACGAGATGACTGTTACTCACATCCTCACTTCCGATGGCCTGCATGCTGAGGGTATTGTCATTGGAACAGGAGAAAATTCTGAATTTGGAGAGGTCTTTAAGATGATGCAGGCAGAAGAAGCACCAAAAACTCCTCTGCAGAAGAGCATGGACCTCTTAGGCAAGCAGCTGTCCTTTTACTCCTTTGGTATAATAGGTATCATCATGTTGGTTGGCTGGTTACTAGGAAAAGACATTCTGGAAATGTTCACTATTAGTGTAAGCTTGGCTGTAGCTGCAATTCCTGAAGGCCTGCCTATTGTGGTCACGGTGACTCTAGCCCTTGGTGTTATGAGAATGGTGAAGAAAAGGGCTATTGTAAAGAAATTGCCTATTGTGGAAACACTGGGCTGCTGTAATGTGATTTGTTCAGATAAAACTGGAACCCTGACGAAGAACGAGATGACTGTTACTCACATCCTCACTTCCGATGGCCTGCATGCTGAG

Peptide sequence:

MMQAEEAPKTPLQKSMDLLGKQLSFYSFGIIGIIMLVGWLLGKDILEMFTISVSLAVAAIPEGLPIVVTVTLALGVMRMVKKRAIVKKLPIVETLGCCNVICSDKTGTLTKNEMTVTHILTSDGLHAEGIVIGTGENSEFGEVFKMMQAEEAPKTPLQKSMDLLGKQLSFYSFGIIGIIMLVGWLLGKDILEMFTISVSLAVAAIPEGLPIVVTVTLALGVMRMVKKRAIVKKLPIVETLGCCNVICSDKTGTLTKNEMTVTHILTSDGLHAE

IRESfinder result

IRESfinder score

0.530622298

IRES/non IRES

IRES

riboCIRC information

riboCIRC ID

NA

NA

Evidence
Peptide sequence:

NA

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