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mmu_circAtxn3_397

Basic information of circular RNA
PanCircBase ID:

mmu_circAtxn3_397

mm39_Chr. Position ID:

chr12|101899226|101903728|-

Gene name:

Atxn3

Transcript:

ENSMUST00000021606.12

CircRNA type:

Exonic circular (circ)RNA

Exon/Intron count:

3

Exon/intron indexes:

9,8,7

Exon/intron offsets:

0,1280,4369

Genomic length:

4502

Exon/intron sizes in nt:

9,71,67,133

Flanking exon/introns:

chr12:101892840-101899226|chr12:101903728-101908375

Splice length:

397

Other database IDs:

circAtlas: mmu-Atxn3_0008

circAtlas: hsa-ATXN3_0007

Human Ortholog IDs:
Mature spliced Sequence:

GTTATTCTATATTTGTTGTTAAGGGTGATCTGCCAGATTGTGAAGCTGACCAACTTTTGCAGATGATCAAGGTCCAACAGATGCATCGACCAAAACTTATTGGAGAGGAACTTGCACATCTGAAAGAGCAGAGTGCCCTCAAAGCAGACCTGGAGCGCGTCTTAGAAGCAGCTGATGGGTCGGGCATATTTGATGAAGATGAGGATGATTTACAGAGGGCTCTAGCCATAAGTCGCCAGGAAATCGACATGGAGGATGAAGAAGCTGATCTCCGCAGGGCCATTCAGCTCAGTATGCAAGGTAGTTCCAGAAGTATGTGTGAAAATAGTCCACAGACATCAAGTCCAGATCTCTCTTCAGAAGAGCTGCGGAGGAGACGAGAAGCCTACTTTGAAAA

Divergent primers for circular RNA PCR

Primer Set-1

Forward primer
Tm
Reverse primer
Tm
Product size

CTTCAGAAGAGCTGCGGAGG

60.46

AGTTTTGGTCGATGCATCTGT

58.22

140

Primer Set-2

Forward primer
Tm
Reverse primer
Tm
Product size

TCTTCAGAAGAGCTGCGGAG

59.47

AGTTTTGGTCGATGCATCTGT

58.22

141

PCR template sequence:

AAGGTAGTTCCAGAAGTATGTGTGAAAATAGTCCACAGACATCAAGTCCAGATCTCTCTTCAGAAGAGCTGCGGAGGAGACGAGAAGCCTACTTTGAAAAGTTATTCTATATTTGTTGTTAAGGGTGATCTGCCAGATTGTGAAGCTGACCAACTTTTGCAGATGATCAAGGTCCAACAGATGCATCGACCAAAACTTAT

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

NA

Interacting miRNAs (#binding sites)

NA

siRNAs for circular RNA silencing
Junction sequence

CCTACTTTGAAAAGTTATTCTATATT

siRNA sets

AATATAGAATAACTTTTCA, ATAGAATAACTTTTCAAAG, ATATAGAATAACTTTTCAA

Protein-coding potential of circular RNAs

CPAT analysis

CPAT ORF ID
CPAT Fickett
CPAT Hexamer
Coding probabilty
ORF length

CIRCATXN3_397_ORF_1

1.0285

0.232443766

0.814042685

537

ORF sequence:

ATGAAGAAGCTGATCTCCGCAGGGCCATTCAGCTCAGTATGCAAGGTAGTTCCAGAAGTATGTGTGAAAATAGTCCACAGACATCAAGTCCAGATCTCTCTTCAGAAGAGCTGCGGAGGAGACGAGAAGCCTACTTTGAAAAGTTATTCTATATTTGTTGTTAAGGGTGATCTGCCAGATTGTGAAGCTGACCAACTTTTGCAGATGATCAAGGTCCAACAGATGCATCGACCAAAACTTATTGGAGAGGAACTTGCACATCTGAAAGAGCAGAGTGCCCTCAAAGCAGACCTGGAGCGCGTCTTAGAAGCAGCTGATGGGTCGGGCATATTTGATGAAGATGAGGATGATTTACAGAGGGCTCTAGCCATAAGTCGCCAGGAAATCGACATGGAGGATGAAGAAGCTGATCTCCGCAGGGCCATTCAGCTCAGTATGCAAGGTAGTTCCAGAAGTATGTGTGAAAATAGTCCACAGACATCAAGTCCAGATCTCTCTTCAGAAGAGCTGCGGAGGAGACGAGAAGCCTACTTTGAA

Peptide sequence:

MKKLISAGPFSSVCKVVPEVCVKIVHRHQVQISLQKSCGGDEKPTLKSYSIFVVKGDLPDCEADQLLQMIKVQQMHRPKLIGEELAHLKEQSALKADLERVLEAADGSGIFDEDEDDLQRALAISRQEIDMEDEEADLRRAIQLSMQGSSRSMCENSPQTSSPDLSSEELRRRREAYFE

IRESfinder result

IRESfinder score

0.494902662

IRES/non IRES

non-IRES

riboCIRC information

riboCIRC ID

NA

NA

Evidence
Peptide sequence:

NA

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