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mmu_circCcdc39_677

Basic information of circular RNA
PanCircBase ID:

mmu_circCcdc39_677

mm39_Chr. Position ID:

chr3|33884805|33892113|-

Gene name:

Ccdc39

Transcript:

ENSMUST00000029222.8

CircRNA type:

Exonic circular (circ)RNA

Exon/Intron count:

5

Exon/intron indexes:

8,7,6,5,4

Exon/intron offsets:

0,1871,6059,6283,7149

Genomic length:

7308

Exon/intron sizes in nt:

1,04,19,21,29,93,159

Flanking exon/introns:

chr3:33884306-33884805|chr3:33892113-33893226

Splice length:

677

Other database IDs:

CIRCpedia: MMU_CIRCpedia_17000, circAtlas: mmu-Ccdc39_0003

Human Ortholog IDs:
Mature spliced Sequence:

AACAATATATTTAAAACTACTCAAAAGCTGGATGACTTGAAATGTCAGATGAACTGGGACCAGCAAGCCTTGGAGGCCTGGCTGGAAGAATCGGCTCACAAAGACAGTGACTCTCTGACCCTTCAGAAGTACTCTCAGCAAGACGATAACAAAATCAGGGCCCTGACTCTGCAGTTAGAAAAGCTGACCATGGAGTATAACGAGAAGAGGAAGCTTCTAGACAGTGAACTGACAGAGACGCTAAGTGCGCAGTTAGAATTAGATAAAGCTGCACAGGATTTCCGGAAGATTCACTTAGAACGGCAGGAGCTCATTCAGCAGTGGGAGAACACCATTGAGCAGATGCAGAGGCGGGATCAGGAGATAGACAACTGTGCCCTGGCATTATCACGAATAAAGCAGGAAGCAAGAGAAAAAGAAGGCGTGGTGAAAGAGAAGATCAAGTTTCTGGAAAATGAGGTTGAGAACAACATAGAATACGAGAGAAAAATTTCTGTTGCTGAGCGGAAAGTGTCCAAGTGCAGGATGGACTACCAGCGTCACGAAGGCAACAGAAGTCAGCTGAAGGATGAGCTGGATACTTTAAAAACCACTCTCAACAGAACATCCAGTGACTTACAAGCTCTGAGGAAAAACATTTCCAAAGTAAAGAAGGACATCTTTGACGAAACATTAAG

Divergent primers for circular RNA PCR

Primer Set-1

Forward primer
Tm
Reverse primer
Tm
Product size

ACCACTCTCAACAGAACATCCA

59.29

TGCTGGTCCCAGTTCATCTG

59.67

154

Primer Set-2

Forward primer
Tm
Reverse primer
Tm
Product size

ACCACTCTCAACAGAACATCCA

59.29

GCTTGCTGGTCCCAGTTCAT

60.61

157

PCR template sequence:

ATACTTTAAAAACCACTCTCAACAGAACATCCAGTGACTTACAAGCTCTGAGGAAAAACATTTCCAAAGTAAAGAAGGACATCTTTGACGAAACATTAAGAACAATATATTTAAAACTACTCAAAAGCTGGATGACTTGAAATGTCAGATGAACTGGGACCAGCAAGCCTTGGAGGCCTGGCTGGAAGAATCGGCTCACA

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

4

Interacting miRNAs (#binding sites)

mmu-miR-140-5p(1), mmu-miR-224-5p(1), mmu-miR-802-5p(1), mmu-miR-540-3p(1)

siRNAs for circular RNA silencing
Junction sequence

ACGAAACATTAAGAACAATATATTTA

siRNA sets

AAATATATTGTTCTTAATG, TAAATATATTGTTCTTAAT, ATTGTTCTTAATGTTTCGT

Protein-coding potential of circular RNAs

CPAT analysis

CPAT ORF ID
CPAT Fickett
CPAT Hexamer
Coding probabilty
ORF length

CIRCCCDC39_677_ORF_1

1.0844

0.331212659

0.949007771

669

ORF sequence:

ATGAACTGGGACCAGCAAGCCTTGGAGGCCTGGCTGGAAGAATCGGCTCACAAAGACAGTGACTCTCTGACCCTTCAGAAGTACTCTCAGCAAGACGATAACAAAATCAGGGCCCTGACTCTGCAGTTAGAAAAGCTGACCATGGAGTATAACGAGAAGAGGAAGCTTCTAGACAGTGAACTGACAGAGACGCTAAGTGCGCAGTTAGAATTAGATAAAGCTGCACAGGATTTCCGGAAGATTCACTTAGAACGGCAGGAGCTCATTCAGCAGTGGGAGAACACCATTGAGCAGATGCAGAGGCGGGATCAGGAGATAGACAACTGTGCCCTGGCATTATCACGAATAAAGCAGGAAGCAAGAGAAAAAGAAGGCGTGGTGAAAGAGAAGATCAAGTTTCTGGAAAATGAGGTTGAGAACAACATAGAATACGAGAGAAAAATTTCTGTTGCTGAGCGGAAAGTGTCCAAGTGCAGGATGGACTACCAGCGTCACGAAGGCAACAGAAGTCAGCTGAAGGATGAGCTGGATACTTTAAAAACCACTCTCAACAGAACATCCAGTGACTTACAAGCTCTGAGGAAAAACATTTCCAAAGTAAAGAAGGACATCTTTGACGAAACATTAAGAACAATATATTTAAAACTACTCAAAAGCTGGATGACTTGA

Peptide sequence:

MNWDQQALEAWLEESAHKDSDSLTLQKYSQQDDNKIRALTLQLEKLTMEYNEKRKLLDSELTETLSAQLELDKAAQDFRKIHLERQELIQQWENTIEQMQRRDQEIDNCALALSRIKQEAREKEGVVKEKIKFLENEVENNIEYERKISVAERKVSKCRMDYQRHEGNRSQLKDELDTLKTTLNRTSSDLQALRKNISKVKKDIFDETLRTIYLKLLKSWMT

IRESfinder result

IRESfinder score

0.511652044

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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