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mmu_circApobec1_348
Basic information of circular RNA
PanCircBase ID:
mmu_circApobec1_348
mm39_Chr. Position ID:
chr6|122565103|122573736|-
Gene name:
Apobec1
Transcript:
ENSMUST00000112586.8
CircRNA type:
Exonic circular (circ)RNA
Exon/Intron count:
3
Exon/intron indexes:
5,4,3
Exon/intron offsets:
0,2942,8487
Genomic length:
8633
Exon/intron sizes in nt:
28,174,146
Flanking exon/introns:
chr6:122558709-122565103|chr6:122573736-122577016
Splice length:
348
Other database IDs:
circAtlas: mmu-Apobec1_0001
Human Ortholog IDs:
Mature spliced Sequence:
GACTGCTAGACACACTGGAGAGAAGCTGCTTCCGTCTGCCCTGCGTCTGTAGAGTGTCCAGCATCCTGACCCATGAATCAGAGACTACTGTCTGATTTGCCTTGACTCAGAGAGTCTGAACCTGACCTTCAGCTAACCTCACACAGTACAGATCTCAAGTTGCTACTGACGCTCAGGAATGAGTCACCCCGTGTCCCTGCAGGTGGCTGTGGGCACACCTGAGGAAACAAAGTCCGGCACACAGCTGGCAGAAGCCATCGCAGCAACATAAGCTCCCGAGGAAGGCGTCCAGAGACAGAGCAAGATGAGTTCCGAGACAGGCCCTGTAGCTGTTGATCCCACTCTGAG
Divergent primers for circular RNA PCR
Primer Set-1
Forward primer
Tm
Reverse primer
Tm
Product size
GCAACATAAGCTCCCGAGGA
59.82
GGTCAGGATGCTGGACACTC
60.11
157
Primer Set-2
Forward primer
Tm
Reverse primer
Tm
Product size
AGCAACATAAGCTCCCGAGG
59.82
GGTCAGGATGCTGGACACTC
60.11
158
PCR template sequence:
CAGAAGCCATCGCAGCAACATAAGCTCCCGAGGAAGGCGTCCAGAGACAGAGCAAGATGAGTTCCGAGACAGGCCCTGTAGCTGTTGATCCCACTCTGAGGACTGCTAGACACACTGGAGAGAAGCTGCTTCCGTCTGCCCTGCGTCTGTAGAGTGTCCAGCATCCTGACCCATGAATCAGAGACTACTGTCTGATTTGC
Note: Users can design additional primers for provided template sequence using Primer3 or NCBI primer-blast.
miRNAs associated with circular RNAs
No of miRNAs
5
Interacting miRNAs (#binding sites)
mmu-miR-135a-5p(1), mmu-miR-326-3p(1), mmu-miR-199b-3p(1), mmu-miR-199a-3p(1), mmu-miR-3470b(1)
siRNAs for circular RNA silencing
Junction sequence
ATCCCACTCTGAGGACTGCTAGACAC
siRNA sets
TGTCTAGCAGTCCTCAGAG, TCTAGCAGTCCTCAGAGTG
Protein-coding potential of circular RNAs
CPAT analysis
CPAT ORF ID
CPAT Fickett
CPAT Hexamer
Coding probabilty
ORF length
CIRCAPOBEC1_348_ORF_1
1.1545
0.07881686
0.109350256
96
ORF sequence:
ATGAGTTCCGAGACAGGCCCTGTAGCTGTTGATCCCACTCTGAGGACTGCTAGACACACTGGAGAGAAGCTGCTTCCGTCTGCCCTGCGTCTGTAG
Peptide sequence:
MSSETGPVAVDPTLRTARHTGEKLLPSALRL
IRESfinder result
IRESfinder score
0.556014369
IRES/non IRES
IRES
riboCIRC information
riboCIRC ID
NA
NA
Evidence
Peptide sequence:
NA
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