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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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