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mmu_circAtg2b_316
Basic information of circular RNA
PanCircBase ID:
mmu_circAtg2b_316
mm39_Chr. Position ID:
chr12|105637734|105641272|-
Gene name:
Atg2b
Transcript:
ENSMUST00000041055.9
CircRNA type:
Exonic circular (circ)RNA
Exon/Intron count:
2
Exon/intron indexes:
3,2
Exon/intron offsets:
0,3375
Genomic length:
3538
Exon/intron sizes in nt:
153,163
Flanking exon/introns:
chr12:105637036-105637734|chr12:105641272-105650927
Splice length:
316
Other database IDs:
CIRCpedia: MMU_CIRCpedia_1520, circAtlas: mmu-Atg2b_0011
Human Ortholog IDs:
Mature spliced Sequence:
TGTCTCAATGAAATCCTGGAGTCAGCAGATGCACCATTAGAAGTCACTGAAGGATTTATTCAGTCCATTTCCCTGTCCGTCCCATGGGGCTCCTTGCTGCAGGACAACTGTGCCCTGGAAGTGAGAGGACTGGAGATGGTCTTCCGGCCTCGACCTCGAGTAGCAACTGGGTCCGAGCCTATGTACTGGTCAAGCTTCATGACCAGCAGTATGCAGCTGGCAAAGGAGTGCCTTAGCCAGAAACTGACAGATGAGCAAGGAGAGGCATCCCAACCTTTCGAGGGACTGGAAAAGTTTGCAGAAACCATCGAAACAG
Divergent primers for circular RNA PCR
Primer Set-1
Forward primer
Tm
Reverse primer
Tm
Product size
AGGCATCCCAACCTTTCGAG
60.04
CATGGGACGGACAGGGAAAT
59.74
140
Primer Set-2
Forward primer
Tm
Reverse primer
Tm
Product size
AGAGGCATCCCAACCTTTCG
60.04
ATGGGACGGACAGGGAAATG
59.74
141
PCR template sequence:
CTGGCAAAGGAGTGCCTTAGCCAGAAACTGACAGATGAGCAAGGAGAGGCATCCCAACCTTTCGAGGGACTGGAAAAGTTTGCAGAAACCATCGAAACAGTGTCTCAATGAAATCCTGGAGTCAGCAGATGCACCATTAGAAGTCACTGAAGGATTTATTCAGTCCATTTCCCTGTCCGTCCCATGGGGCTCCTTGCTGC
Note: Users can design additional primers for provided template sequence using Primer3 or NCBI primer-blast.
miRNAs associated with circular RNAs
No of miRNAs
3
Interacting miRNAs (#binding sites)
mmu-miR-200b-3p(1), mmu-miR-680(1), mmu-miR-207(1)
siRNAs for circular RNA silencing
Junction sequence
ACCATCGAAACAGTGTCTCAATGAAA
siRNA sets
TTTCATTGAGACACTGTTT
Protein-coding potential of circular RNAs
CPAT analysis
CPAT ORF ID
CPAT Fickett
CPAT Hexamer
Coding probabilty
ORF length
CIRCATG2B_316_ORF_1
0.8434
0.273107183
0.544023027
381
ORF sequence:
ATGAGCAAGGAGAGGCATCCCAACCTTTCGAGGGACTGGAAAAGTTTGCAGAAACCATCGAAACAGTGTCTCAATGAAATCCTGGAGTCAGCAGATGCACCATTAGAAGTCACTGAAGGATTTATTCAGTCCATTTCCCTGTCCGTCCCATGGGGCTCCTTGCTGCAGGACAACTGTGCCCTGGAAGTGAGAGGACTGGAGATGGTCTTCCGGCCTCGACCTCGAGTAGCAACTGGGTCCGAGCCTATGTACTGGTCAAGCTTCATGACCAGCAGTATGCAGCTGGCAAAGGAGTGCCTTAGCCAGAAACTGACAGATGAGCAAGGAGAGGCATCCCAACCTTTCGAGGGACTGGAAAAGTTTGCAGAAACCATCGAAACA
Peptide sequence:
MSKERHPNLSRDWKSLQKPSKQCLNEILESADAPLEVTEGFIQSISLSVPWGSLLQDNCALEVRGLEMVFRPRPRVATGSEPMYWSSFMTSSMQLAKECLSQKLTDEQGEASQPFEGLEKFAETIET
IRESfinder result
IRESfinder score
0.528890805
IRES/non IRES
IRES
riboCIRC information
riboCIRC ID
NA
NA
Evidence
Peptide sequence:
NA
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