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mmu_circRfc1_847

Basic information of circular RNA
PanCircBase ID:

mmu_circRfc1_847

mm39_Chr. Position ID:

chr5|65453296|65476873|-

Gene name:

Rfc1

Transcript:

ENSMUST00000203581.3

CircRNA type:

Exonic circular (circ)RNA

Exon/Intron count:

7

Exon/intron indexes:

8,7,6,5,4,3,2

Exon/intron offsets:

0,1445,5979,7022,15087,17004,23451

Genomic length:

23577

Exon/intron sizes in nt:

9,17,81,20,23,31,23,76,000

Flanking exon/introns:

chr5:65451278-65453296|chr5:65476873-65492866

Splice length:

847

Other database IDs:

circAtlas: mmu-Rfc1_0048

Human Ortholog IDs:
Mature spliced Sequence:

GACATTCGGAAATTCTTTGGGGTTATATCAAGTGGAAAAAAGCCTGTAAACGAGACAGTAAAGAATGAGAAGACAAAAGCTTCGGAGGGAACTGTCAAAGGAAAAAAGGGAGTCAAGGAGGCCAAGGTCAATAACTCCGGTAAAGAGGACGCCTCCAAACCAAAGCAGCACAGCAAGAAGAAGAGGATCATCAATGACTCAGACTCAGAGTCAGAGGAGACAGTACAGGTAAAAAATGCTAAAAAGAAATCAGAAAAATTGTCACTGTCTTATAAACCTGGTAAAGTCTCTCAGAAGGATCCTGTCACCTACGTCTCTGAGACAGATGAAGATGATGACTTTGTATGTAAAAAGGCAGCCTCCAAATCAAAAGAGAATGGAGTATCTACAAATAGTTACCTTGGAACATCAAACGTGAAAAAAAATGAAGAAAACGTTAAGACTAAGAACAAGCCGTTATCTCCAATAAAACTCACACCAACGTCAGTGCTCGACTATTTTGGAACTGAAAGTGTCCAGAGATCTGGGAAGAAGATGGTGACAAGCAAAAGGAAAGAACCAGATTTCTGCTTATCTTGCTTGATTTTCTTTGGAATACAGTCTTCTCAAAACACAGAGGATTCCAGATTAAATGATGAGGCCATCGCCAAGCAGCTGCAGCTGGATGAAGATGCAGAGCTGGAGAGGCAGTTGCATGAAGATGAAGAATTTGCAAGAACACTGGCCTTATTGGATGAAGAACCCAAGATCAAAAAGGCCCGAAAGGATTCTGAAGAGGGAGAAGAATCATTTTCATCTGTCCAAGATGATTTAAGCAAAGCAGAAAAGCAGAAAAGCCCTAATAAAG

Divergent primers for circular RNA PCR

Primer Set-1

Forward primer
Tm
Reverse primer
Tm
Product size

CGAAAGGATTCTGAAGAGGGAGA

59.55

TCCCTCCGAAGCTTTTGTCT

58.94

178

Primer Set-2

Forward primer
Tm
Reverse primer
Tm
Product size

AGGATTCTGAAGAGGGAGAAGA

57.66

GACAGTTCCCTCCGAAGCTT

59.68

180

PCR template sequence:

ATCAAAAAGGCCCGAAAGGATTCTGAAGAGGGAGAAGAATCATTTTCATCTGTCCAAGATGATTTAAGCAAAGCAGAAAAGCAGAAAAGCCCTAATAAAGGACATTCGGAAATTCTTTGGGGTTATATCAAGTGGAAAAAAGCCTGTAAACGAGACAGTAAAGAATGAGAAGACAAAAGCTTCGGAGGGAACTGTCAAAG

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

10

Interacting miRNAs (#binding sites)

mmu-miR-9-5p(1), mmu-miR-199a-5p(1), mmu-miR-211-5p(1), mmu-miR-204-5p(1), mmu-miR-136-5p(1), mmu-miR-34b-5p(1), mmu-miR-325-3p(1), mmu-miR-1199-5p(1), mmu-miR-466b-3p(1), mmu-miR-1904(1)

siRNAs for circular RNA silencing
Junction sequence

AGCCCTAATAAAGGACATTCGGAAAT

siRNA sets

ATTTCCGAATGTCCTTTAT, TTTCCGAATGTCCTTTATT

Protein-coding potential of circular RNAs

CPAT analysis

CPAT ORF ID
CPAT Fickett
CPAT Hexamer
Coding probabilty
ORF length

CIRCRFC1_847_ORF_1

0.779

0.196532354

0.430182204

381

ORF sequence:

ATGGTGACAAGCAAAAGGAAAGAACCAGATTTCTGCTTATCTTGCTTGATTTTCTTTGGAATACAGTCTTCTCAAAACACAGAGGATTCCAGATTAAATGATGAGGCCATCGCCAAGCAGCTGCAGCTGGATGAAGATGCAGAGCTGGAGAGGCAGTTGCATGAAGATGAAGAATTTGCAAGAACACTGGCCTTATTGGATGAAGAACCCAAGATCAAAAAGGCCCGAAAGGATTCTGAAGAGGGAGAAGAATCATTTTCATCTGTCCAAGATGATTTAAGCAAAGCAGAAAAGCAGAAAAGCCCTAATAAAGGACATTCGGAAATTCTTTGGGGTTATATCAAGTGGAAAAAAGCCTGTAAACGAGACAGTAAAGAATGA

Peptide sequence:

MVTSKRKEPDFCLSCLIFFGIQSSQNTEDSRLNDEAIAKQLQLDEDAELERQLHEDEEFARTLALLDEEPKIKKARKDSEEGEESFSSVQDDLSKAEKQKSPNKGHSEILWGYIKWKKACKRDSKE

IRESfinder result

IRESfinder score

0.448234415

IRES/non IRES

non-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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