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mmu_circArhgef12_435

Basic information of circular RNA
PanCircBase ID:

mmu_circArhgef12_435

mm39_Chr. Position ID:

chr9|42929347|42934168|-

Gene name:

Arhgef12

Transcript:

ENSMUST00000165665.9

CircRNA type:

Exonic circular (circ)RNA

Exon/Intron count:

4

Exon/intron indexes:

10,9,8,7

Exon/intron offsets:

0,283,2553,4763

Genomic length:

4821

Exon/intron sizes in nt:

120,78,179,58

Flanking exon/introns:

chr9:42927339-42929347|chr9:42934168-42937475

Splice length:

435

Other database IDs:

Human Ortholog IDs:
Mature spliced Sequence:

GTGAATGGTACTCTGGTGACTCATTCAAATCATCTGGAGGTGGTGAAACTAATCAGATCTGGTTCCTATGTAGCTCTCACTGTCCAGGGACGCCCACCTGGGTCGCCCCAGATCCCACTTGCTGATTCTGAAGTAGAGCCATCAGTCACTGGACATATGTCTCCCATTATGACATCCCCTCATTCCCCTGGAGCAGCCGGGAATATGGAGAGAATCACCAGTCCTGTGCTCGTGGGGGAGGAAAACAATGTGGTCCATAACCAGAAAGTAGAGATTCTGAGAAAGATGTTACAGAAGGAACAGGAACGGCTGCAGTTGCTGCAGGAAGATTACAACCGAACGGCTACCCAAAGATTGCTCAAGGAGATCCAGGAGGCCAAGAAGCACATCCCGCAGCTGCAGGAGCAGCTGTCCAAAGCCACGGGCTCTGCTCAG

Divergent primers for circular RNA PCR

Primer Set-1

Forward primer
Tm
Reverse primer
Tm
Product size

AGGAGGCCAAGAAGCACATC

60.03

TCCCTGGACAGTGAGAGCTA

59.3

155

Primer Set-2

Forward primer
Tm
Reverse primer
Tm
Product size

AGGAGGCCAAGAAGCACATC

60.03

CCCTGGACAGTGAGAGCTAC

59.18

154

PCR template sequence:

CCGAACGGCTACCCAAAGATTGCTCAAGGAGATCCAGGAGGCCAAGAAGCACATCCCGCAGCTGCAGGAGCAGCTGTCCAAAGCCACGGGCTCTGCTCAGGTGAATGGTACTCTGGTGACTCATTCAAATCATCTGGAGGTGGTGAAACTAATCAGATCTGGTTCCTATGTAGCTCTCACTGTCCAGGGACGCCCACCTG

Note: Users can design additional primers for provided template sequence using Primer3 or NCBI primer-blast.
miRNAs associated with circular RNAs
No of miRNAs

1

Interacting miRNAs (#binding sites)

mmu-miR-222-3p(1)

siRNAs for circular RNA silencing
Junction sequence

GGGCTCTGCTCAGGTGAATGGTACTC

siRNA sets

ATTCACCTGAGCAGAGCCC, TACCATTCACCTGAGCAGA, AGTACCATTCACCTGAGCA

Protein-coding potential of circular RNAs

CPAT analysis

CPAT ORF ID
CPAT Fickett
CPAT Hexamer
Coding probabilty
ORF length

CIRCARHGEF12_435_ORF_1

1.2538

0.357887119

0.975490623

714

ORF sequence:

ATGTCTCCCATTATGACATCCCCTCATTCCCCTGGAGCAGCCGGGAATATGGAGAGAATCACCAGTCCTGTGCTCGTGGGGGAGGAAAACAATGTGGTCCATAACCAGAAAGTAGAGATTCTGAGAAAGATGTTACAGAAGGAACAGGAACGGCTGCAGTTGCTGCAGGAAGATTACAACCGAACGGCTACCCAAAGATTGCTCAAGGAGATCCAGGAGGCCAAGAAGCACATCCCGCAGCTGCAGGAGCAGCTGTCCAAAGCCACGGGCTCTGCTCAGGTGAATGGTACTCTGGTGACTCATTCAAATCATCTGGAGGTGGTGAAACTAATCAGATCTGGTTCCTATGTAGCTCTCACTGTCCAGGGACGCCCACCTGGGTCGCCCCAGATCCCACTTGCTGATTCTGAAGTAGAGCCATCAGTCACTGGACATATGTCTCCCATTATGACATCCCCTCATTCCCCTGGAGCAGCCGGGAATATGGAGAGAATCACCAGTCCTGTGCTCGTGGGGGAGGAAAACAATGTGGTCCATAACCAGAAAGTAGAGATTCTGAGAAAGATGTTACAGAAGGAACAGGAACGGCTGCAGTTGCTGCAGGAAGATTACAACCGAACGGCTACCCAAAGATTGCTCAAGGAGATCCAGGAGGCCAAGAAGCACATCCCGCAGCTGCAGGAGCAGCTGTCCAAAGCCACGGGCTCTGCTCAG

Peptide sequence:

MSPIMTSPHSPGAAGNMERITSPVLVGEENNVVHNQKVEILRKMLQKEQERLQLLQEDYNRTATQRLLKEIQEAKKHIPQLQEQLSKATGSAQVNGTLVTHSNHLEVVKLIRSGSYVALTVQGRPPGSPQIPLADSEVEPSVTGHMSPIMTSPHSPGAAGNMERITSPVLVGEENNVVHNQKVEILRKMLQKEQERLQLLQEDYNRTATQRLLKEIQEAKKHIPQLQEQLSKATGSAQ

IRESfinder result

IRESfinder score

0.484564471

IRES/non IRES

non-IRES

riboCIRC information

riboCIRC ID

NA

NA

Evidence
Peptide sequence:

NA

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