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mmu_circZfyve9_678

Basic information of circular RNA
PanCircBase ID:

mmu_circZfyve9_678

mm39_Chr. Position ID:

chr4|108499284|108517912|-

Gene name:

Zfyve9

Transcript:

ENSMUST00000106658.8

CircRNA type:

Exonic circular (circ)RNA

Exon/Intron count:

5

Exon/intron indexes:

17,16,15,14,13

Exon/intron offsets:

0,2248,8096,14839,18477

Genomic length:

18628

Exon/intron sizes in nt:

1,77,10,61,63,81,151

Flanking exon/introns:

chr4:108496617-108499284|chr4:108517912-108531649

Splice length:

678

Other database IDs:

circAtlas: mmu-Zfyve9_0051

Human Ortholog IDs:
Mature spliced Sequence:

ATGATGAAAGCCATGAACAAATCCAATGAACATGTACTGGCAGGAGGTGCCTGCTTCAATGAAAAGGCAGATTCTCATCTTGTGTGTGTACAGAACGATGATGGAAACTATCAAACCCAGGCCATCAGTATTCACAATCAGCCCAGGAAAGTGACTGGCGCCAGTTTCTTTGTGTTCAGTGGCGCACTGAAATCCTCTTCAGGATACCTTGCCAAGTCCAGTATTGTAGAAGATGGAGTCATGGTCCAGATCACTGCGGAGAACATGGACTCCTTGAGGCAGGCACTGCGGGAGATGAAGGACTTTACCATCACTTGTGGGAAGGCGGATGCAGAGGACCCCCAGGAACAGATCCACATCCAGTGGGTGGACGATGACAAGACAGTTAACAAAGGTGTGGTGAGTCCTATAGATGGGAAGTCTATGGAATCTATAACAAACGTGAAAATATTCCATGGGTCAGAGTATAAAGCAAACGGAAAAGTCATCAGATGGACAGAGGTGTTTTTCCTGGAAAACGATGACCACCATAACTGCCTGAGTGACCCTGCAGATCACAGCAGACTGACTGAGCATGTCGCCAAGGCATTCTGCCTCGCCCTCTGCCCCCACCTGAAGCTTTTAAAAGAAGATGGAATGACAAAACTGGGACTCCGTGTGACGCTTGACTCAGATCAG

Divergent primers for circular RNA PCR

Primer Set-1

Forward primer
Tm
Reverse primer
Tm
Product size

GCCCCCACCTGAAGCTTTTA

60.25

GCCTTTTCATTGAAGCAGGCA

60

142

Primer Set-2

Forward primer
Tm
Reverse primer
Tm
Product size

GCCCCCACCTGAAGCTTTTA

60.25

TGCCTTTTCATTGAAGCAGGC

60

143

PCR template sequence:

CGCCAAGGCATTCTGCCTCGCCCTCTGCCCCCACCTGAAGCTTTTAAAAGAAGATGGAATGACAAAACTGGGACTCCGTGTGACGCTTGACTCAGATCAGATGATGAAAGCCATGAACAAATCCAATGAACATGTACTGGCAGGAGGTGCCTGCTTCAATGAAAAGGCAGATTCTCATCTTGTGTGTGTACAGAACGATG

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-429-3p(1), mmu-miR-200b-3p(1), mmu-miR-200c-3p(1), mmu-miR-205-5p(1), mmu-miR-182-5p(1), mmu-miR-1199-5p(1)

siRNAs for circular RNA silencing
Junction sequence

TGACTCAGATCAGATGATGAAAGCCA

siRNA sets

TTTCATCATCTGATCTGAG,TTCATCATCTGATCTGAGT,CTTTCATCATCTGATCTGA

Protein-coding potential of circular RNAs

CPAT analysis

CPAT ORF ID
CPAT Fickett
CPAT Hexamer
Coding probabilty
ORF length

CIRCZFYVE9_678_ORF_1

1.2107

0.265554492

0.999609525

1356

ORF sequence:

ATGATGAAAGCCATGAACAAATCCAATGAACATGTACTGGCAGGAGGTGCCTGCTTCAATGAAAAGGCAGATTCTCATCTTGTGTGTGTACAGAACGATGATGGAAACTATCAAACCCAGGCCATCAGTATTCACAATCAGCCCAGGAAAGTGACTGGCGCCAGTTTCTTTGTGTTCAGTGGCGCACTGAAATCCTCTTCAGGATACCTTGCCAAGTCCAGTATTGTAGAAGATGGAGTCATGGTCCAGATCACTGCGGAGAACATGGACTCCTTGAGGCAGGCACTGCGGGAGATGAAGGACTTTACCATCACTTGTGGGAAGGCGGATGCAGAGGACCCCCAGGAACAGATCCACATCCAGTGGGTGGACGATGACAAGACAGTTAACAAAGGTGTGGTGAGTCCTATAGATGGGAAGTCTATGGAATCTATAACAAACGTGAAAATATTCCATGGGTCAGAGTATAAAGCAAACGGAAAAGTCATCAGATGGACAGAGGTGTTTTTCCTGGAAAACGATGACCACCATAACTGCCTGAGTGACCCTGCAGATCACAGCAGACTGACTGAGCATGTCGCCAAGGCATTCTGCCTCGCCCTCTGCCCCCACCTGAAGCTTTTAAAAGAAGATGGAATGACAAAACTGGGACTCCGTGTGACGCTTGACTCAGATCAGATGATGAAAGCCATGAACAAATCCAATGAACATGTACTGGCAGGAGGTGCCTGCTTCAATGAAAAGGCAGATTCTCATCTTGTGTGTGTACAGAACGATGATGGAAACTATCAAACCCAGGCCATCAGTATTCACAATCAGCCCAGGAAAGTGACTGGCGCCAGTTTCTTTGTGTTCAGTGGCGCACTGAAATCCTCTTCAGGATACCTTGCCAAGTCCAGTATTGTAGAAGATGGAGTCATGGTCCAGATCACTGCGGAGAACATGGACTCCTTGAGGCAGGCACTGCGGGAGATGAAGGACTTTACCATCACTTGTGGGAAGGCGGATGCAGAGGACCCCCAGGAACAGATCCACATCCAGTGGGTGGACGATGACAAGACAGTTAACAAAGGTGTGGTGAGTCCTATAGATGGGAAGTCTATGGAATCTATAACAAACGTGAAAATATTCCATGGGTCAGAGTATAAAGCAAACGGAAAAGTCATCAGATGGACAGAGGTGTTTTTCCTGGAAAACGATGACCACCATAACTGCCTGAGTGACCCTGCAGATCACAGCAGACTGACTGAGCATGTCGCCAAGGCATTCTGCCTCGCCCTCTGCCCCCACCTGAAGCTTTTAAAAGAAGATGGAATGACAAAACTGGGACTCCGTGTGACGCTTGACTCAGATCAG

Peptide sequence:

MMKAMNKSNEHVLAGGACFNEKADSHLVCVQNDDGNYQTQAISIHNQPRKVTGASFFVFSGALKSSSGYLAKSSIVEDGVMVQITAENMDSLRQALREMKDFTITCGKADAEDPQEQIHIQWVDDDKTVNKGVVSPIDGKSMESITNVKIFHGSEYKANGKVIRWTEVFFLENDDHHNCLSDPADHSRLTEHVAKAFCLALCPHLKLLKEDGMTKLGLRVTLDSDQMMKAMNKSNEHVLAGGACFNEKADSHLVCVQNDDGNYQTQAISIHNQPRKVTGASFFVFSGALKSSSGYLAKSSIVEDGVMVQITAENMDSLRQALREMKDFTITCGKADAEDPQEQIHIQWVDDDKTVNKGVVSPIDGKSMESITNVKIFHGSEYKANGKVIRWTEVFFLENDDHHNCLSDPADHSRLTEHVAKAFCLALCPHLKLLKEDGMTKLGLRVTLDSDQ

IRESfinder result

IRESfinder score

0.458595662

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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