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mmu_circMarchf8_211
Basic information of circular RNA
PanCircBase ID:
mmu_circMarchf8_211
mm39_Chr. Position ID:
chr6|116353096|116353824|+
Gene name:
Marchf8
Transcript:
ENSMUST00000129170.8
CircRNA type:
Exonic circular (circ)RNA
Exon/Intron count:
2
Exon/intron indexes:
2,3
Exon/intron offsets:
0,557
Genomic length:
728
Exon/intron sizes in nt:
40,171
Flanking exon/introns:
chr6:116327917-116353096|None
Splice length:
211
Other database IDs:
CIRCpedia: MMU_CIRCpedia_4060
Human Ortholog IDs:
Mature spliced Sequence:
CTTCATACTAGGGATTGAACCCAGGGACTTGGGTATATAGCTTGAAGTCAATGGCCCAAAATGACTCTGCTAGAGGAGACTCACTTCCGTAAGGAGGAAGACCAGGTCGGAGGCTGGGATGAGCATGCCATTGCACCAGATCTCTGCCATCCCTTCTCAGGATGCCATTTCTGCTAGAGTCTACAGAAGCAAGACCAAAGATAAGGAGCAG
Divergent primers for circular RNA PCR
Primer Set-1
Forward primer
Tm
Reverse primer
Tm
Product size
ACCAGATCTCTGCCATCCCT
60.03
AGCAGAGTCATTTTGGGCCA
59.89
148
Primer Set-2
Forward primer
Tm
Reverse primer
Tm
Product size
TCTGCCATCCCTTCTCAGGA
59.96
AGCAGAGTCATTTTGGGCCA
59.89
140
PCR template sequence:
GGCTGGGATGAGCATGCCATTGCACCAGATCTCTGCCATCCCTTCTCAGGATGCCATTTCTGCTAGAGTCTACAGAAGCAAGACCAAAGATAAGGAGCAGCTTCATACTAGGGATTGAACCCAGGGACTTGGGTATATAGCTTGAAGTCAATGGCCCAAAATGACTCTGCTAGAGGAGACTCACTTCCGTAAGGAGGAAG
Note: Users can design additional primers for provided template sequence using Primer3 or NCBI primer-blast.
miRNAs associated with circular RNAs
No of miRNAs
2
Interacting miRNAs (#binding sites)
mmu-miR-9-5p(1), mmu-miR-301b-3p(1)
siRNAs for circular RNA silencing
Junction sequence
AGATAAGGAGCAGCTTCATACTAGGG
siRNA sets
TATGAAGCTGCTCCTTATC,CCTAGTATGAAGCTGCTCC,CTAGTATGAAGCTGCTCCT
Protein-coding potential of circular RNAs
CPAT analysis
CPAT ORF ID
CPAT Fickett
CPAT Hexamer
Coding probabilty
ORF length
CIRCMARCHF8_211_ORF_3
1.0332
0.151749648
0.12896428
111
ORF sequence:
ATGAGCATGCCATTGCACCAGATCTCTGCCATCCCTTCTCAGGATGCCATTTCTGCTAGAGTCTACAGAAGCAAGACCAAAGATAAGGAGCAGCTTCATACTAGGGATTGA
Peptide sequence:
MSMPLHQISAIPSQDAISARVYRSKTKDKEQLHTRD
IRESfinder result
IRESfinder score
0.240061855
IRES/non IRES
non-IRES
riboCIRC information
riboCIRC ID
NA
NA
Evidence
Peptide sequence:
NA
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