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mmu_circFndc3b_351

Basic information of circular RNA
PanCircBase ID:

mmu_circFndc3b_351

mm39_Chr. Position ID:

chr3|27545173|27555694|-

Gene name:

Fndc3b

Transcript:

ENSMUST00000195008.6

CircRNA type:

Exonic circular (circ)RNA

Exon/Intron count:

3

Exon/intron indexes:

11,10,9

Exon/intron offsets:

0,7752,10369

Genomic length:

10521

Exon/intron sizes in nt:

1,39,60,152

Flanking exon/introns:

chr3:27542439-27545173|chr3:27555694-27562629

Splice length:

351

Other database IDs:

CIRCpedia: MMU_CIRCpedia_38238, circAtlas: mmu-Fndc3b_0018

circAtlas: hsa-SCAF8_0001, CIRCpedia: HSA_CIRCpedia_105959

Human Ortholog IDs:
Mature spliced Sequence:

GTGTCTAATATCCAGGCAAGAGCAGTTGTGCTGTCTTGGGCACCCCCTGTCGGACTGTCCTGTGGACCCCATGGTGGTCTTTCCTTCCCTTACAGCTATGAGGTCGCCTTATCTGACAAAGGGCGAGATGGGAAATACAAGATCATTTACAGTGGAGAAGAGTTGGAGTGTAACCTGAAAGATCTCAGGCCTGCCACGGATTACCATGTGAGGGTATATGCCGTGTACAATTCTGTCAAGGGATCCTGCTCCGAGCCAGTCAGCTTCACCACCCATAGCTGCGCACCAGAATGTCCCTTCCCTCCCAAGCTGGCACACAGGAGCAAAAGTTCACTTACCCTGCAGTGGAAG

Divergent primers for circular RNA PCR

Primer Set-1

Forward primer
Tm
Reverse primer
Tm
Product size

ATAGCTGCGCACCAGAATGT

60.11

AAGGAAAGACCACCATGGGG

59.59

163

Primer Set-2

Forward primer
Tm
Reverse primer
Tm
Product size

AGAATGTCCCTTCCCTCCCA

59.88

AAGGAAAGACCACCATGGGG

59.59

150

PCR template sequence:

CGAGCCAGTCAGCTTCACCACCCATAGCTGCGCACCAGAATGTCCCTTCCCTCCCAAGCTGGCACACAGGAGCAAAAGTTCACTTACCCTGCAGTGGAAGGTGTCTAATATCCAGGCAAGAGCAGTTGTGCTGTCTTGGGCACCCCCTGTCGGACTGTCCTGTGGACCCCATGGTGGTCTTTCCTTCCCTTACAGCTATG

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-127-5p(1)

siRNAs for circular RNA silencing
Junction sequence

CCTGCAGTGGAAGGTGTCTAATATCC

siRNA sets

TATTAGACACCTTCCACTG, ATATTAGACACCTTCCACT, TTAGACACCTTCCACTGCA

Protein-coding potential of circular RNAs

CPAT analysis

CPAT ORF ID
CPAT Fickett
CPAT Hexamer
Coding probabilty
ORF length

CIRCFNDC3B_351_ORF_1

0.6468

-0.120388562

0.091334552

312

ORF sequence:

ATGCCGTGTACAATTCTGTCAAGGGATCCTGCTCCGAGCCAGTCAGCTTCACCACCCATAGCTGCGCACCAGAATGTCCCTTCCCTCCCAAGCTGGCACACAGGAGCAAAAGTTCACTTACCCTGCAGTGGAAGGTGTCTAATATCCAGGCAAGAGCAGTTGTGCTGTCTTGGGCACCCCCTGTCGGACTGTCCTGTGGACCCCATGGTGGTCTTTCCTTCCCTTACAGCTATGAGGTCGCCTTATCTGACAAAGGGCGAGATGGGAAATACAAGATCATTTACAGTGGAGAAGAGTTGGAGTGTAACCTGA

Peptide sequence:

MPCTILSRDPAPSQSASPPIAAHQNVPSLPSWHTGAKVHLPCSGRCLISRQEQLCCLGHPLSDCPVDPMVVFPSLTAMRSPYLTKGEMGNTRSFTVEKSWSVT

IRESfinder result

IRESfinder score

0.569687421

IRES/non IRES

IRES

riboCIRC information

riboCIRC ID

NA

NA

Evidence
Peptide sequence:

NA

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Institute of Life sciences, Bhubaneswar, India

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