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mmu_circArnt2_439

Basic information of circular RNA
PanCircBase ID:

mmu_circArnt2_439

mm39_Chr. Position ID:

chr7|83931304|83954467|-

Gene name:

Arnt2

Transcript:

ENSMUST00000085077.5

CircRNA type:

Exonic circular (circ)RNA

Exon/Intron count:

5

Exon/intron indexes:

11,10,9,8,7

Exon/intron offsets:

0,1896,3677,22700,23097

Genomic length:

23163

Exon/intron sizes in nt:

75,135,77,86,66

Flanking exon/introns:

chr7:83924694-83931304|chr7:83954467-83960080

Splice length:

439

Other database IDs:

CIRCpedia: MMU_CIRCpedia_31590, circAtlas: mmu-Arnt2_0008

circAtlas: hsa-ARNT2_0008, CIRCpedia: HSA_CIRCpedia_15862

Human Ortholog IDs:
Mature spliced Sequence:

GTGTGGAAACGCTCCCTTGGACCACCTGCCTTTGAACAGAATAACCACCATGAGGAAAAGGTTCAGGAATGGCCTTGGCCCTGTGAAAGAAGGAGAAGCCCAGTATGCTGTGGTCCACTGCACAGGTTACATCAAGGCTTGGCCACCAGCAGGAATGACCATACCCGAAGAAGACGCTGATGTCGGACAAGGCAGTAAATATTGCCTCGTGGCAATTGGGAGGCTCCAGGTGACCAGCTCTCCTGTGTGCATGGACATGAGCGGCATGTCAGTGCCCACAGAGTTCCTGTCACGGCACAACTCTGATGGGATTATCACGTTTGTGGACCCCAGATGCATCAGTGTGATTGGCTACCAGCCCCAGGACCTTCTGGGAAAGGATATTTTGGAATTTTGCCACCCTGAGGATCAGAGCCACCTACGGGAGAGCTTCCAACAG

Divergent primers for circular RNA PCR

Primer Set-1

Forward primer
Tm
Reverse primer
Tm
Product size

CAGTGTGATTGGCTACCAGC

58.91

CCAAGGCCATTCCTGAACCT

59.96

178

Primer Set-2

Forward primer
Tm
Reverse primer
Tm
Product size

GGAATTTTGCCACCCTGAGG

59.1

CTCCTTCTTTCACAGGGCCA

59.6

147

PCR template sequence:

CAGTGTGATTGGCTACCAGCCCCAGGACCTTCTGGGAAAGGATATTTTGGAATTTTGCCACCCTGAGGATCAGAGCCACCTACGGGAGAGCTTCCAACAGGTGTGGAAACGCTCCCTTGGACCACCTGCCTTTGAACAGAATAACCACCATGAGGAAAAGGTTCAGGAATGGCCTTGGCCCTGTGAAAGAAGGAGAAGCC

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

3

Interacting miRNAs (#binding sites)

mmu-miR-411-3p(1), mmu-miR-370-3p(1), mmu-miR-207(1)

siRNAs for circular RNA silencing
Junction sequence

GAGCTTCCAACAGGTGTGGAAACGCT

siRNA sets

NA

Protein-coding potential of circular RNAs

CPAT analysis

CPAT ORF ID
CPAT Fickett
CPAT Hexamer
Coding probabilty
ORF length

CIRCARNT2_439_ORF_1

0.7974

0.17947893

0.743900321

570

ORF sequence:

ATGAGGAAAAGGTTCAGGAATGGCCTTGGCCCTGTGAAAGAAGGAGAAGCCCAGTATGCTGTGGTCCACTGCACAGGTTACATCAAGGCTTGGCCACCAGCAGGAATGACCATACCCGAAGAAGACGCTGATGTCGGACAAGGCAGTAAATATTGCCTCGTGGCAATTGGGAGGCTCCAGGTGACCAGCTCTCCTGTGTGCATGGACATGAGCGGCATGTCAGTGCCCACAGAGTTCCTGTCACGGCACAACTCTGATGGGATTATCACGTTTGTGGACCCCAGATGCATCAGTGTGATTGGCTACCAGCCCCAGGACCTTCTGGGAAAGGATATTTTGGAATTTTGCCACCCTGAGGATCAGAGCCACCTACGGGAGAGCTTCCAACAGGTGTGGAAACGCTCCCTTGGACCACCTGCCTTTGAACAGAATAACCACCATGAGGAAAAGGTTCAGGAATGGCCTTGGCCCTGTGAAAGAAGGAGAAGCCCAGTATGCTGTGGTCCACTGCACAGGTTACATCAAGGCTTGGCCACCAGCAGGAATGACCATACCCGAAGAAGACGCTGA

Peptide sequence:

MRKRFRNGLGPVKEGEAQYAVVHCTGYIKAWPPAGMTIPEEDADVGQGSKYCLVAIGRLQVTSSPVCMDMSGMSVPTEFLSRHNSDGIITFVDPRCISVIGYQPQDLLGKDILEFCHPEDQSHLRESFQQVWKRSLGPPAFEQNNHHEEKVQEWPWPCERRRSPVCCGPLHRLHQGLATSRNDHTRRRR

IRESfinder result

IRESfinder score

0.354623692

IRES/non IRES

non-IRES

riboCIRC information

riboCIRC ID

NA

NA

Evidence
Peptide sequence:

NA

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