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mmu_circMadd_117
Basic information of circular RNA
PanCircBase ID:
mmu_circMadd_117
mm39_Chr. Position ID:
chr2|90969053|90970971|-
Gene name:
Madd
Transcript:
ENSMUST00000111373.8
CircRNA type:
Exonic circular (circ)RNA
Exon/Intron count:
2
Exon/intron indexes:
31,30
Exon/intron offsets:
0,1848
Genomic length:
1918
Exon/intron sizes in nt:
47,70
Flanking exon/introns:
chr2:90968746-90969053|chr2:90970971-90973100
Splice length:
117
Other database IDs:
Human Ortholog IDs:
Mature spliced Sequence:
GTTTTCATAGAGCTGAATCACATTAAAAAGTGCAATACAGTTCGAGGCGTCTTTGTCCTGGAAGAATTTGTTCCTGAAATTAAAGAAGTGGTGAGCCACAAGTACAAGACGCCAATG
Divergent primers for circular RNA PCR
Primer Set-1
Forward primer
Tm
Reverse primer
Tm
Product size
AGCCACAAGTACAAGACGCC
60.6
ACGCCTCGAACTGTATTGCA
60.04
74
Primer Set-2
Forward primer
Tm
Reverse primer
Tm
Product size
AGCCACAAGTACAAGACGCC
60.6
ACAAAGACGCCTCGAACTGT
59.9
80
PCR template sequence:
GGAAGAATTTGTTCCTGAAATTAAAGAAGTGGTGAGCCACAAGTACAAGACGCCAATGGTTTTCATAGAGCTGAATCACATTAAAAAGTGCAATACAGTTCGAGGCGTCTTTGTCC
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-32-5p(1), mmu-miR-92a-3p(1), mmu-miR-25-3p(1)
siRNAs for circular RNA silencing
Junction sequence
CAAGACGCCAATGGTTTTCATAGAGC
siRNA sets
TCTATGAAAACCATTGGCG, CTCTATGAAAACCATTGGC, TATGAAAACCATTGGCGTC
Protein-coding potential of circular RNAs
CPAT analysis
CPAT ORF ID
CPAT Fickett
CPAT Hexamer
Coding probabilty
ORF length
CIRCMADD_117_ORF_1
1.1062
0.248150797
0.21233454
120
ORF sequence:
ATGGTTTTCATAGAGCTGAATCACATTAAAAAGTGCAATACAGTTCGAGGCGTCTTTGTCCTGGAAGAATTTGTTCCTGAAATTAAAGAAGTGGTGAGCCACAAGTACAAGACGCCAATG
Peptide sequence:
MVFIELNHIKKCNTVRGVFVLEEFVPEIKEVVSHKYKTPM
IRESfinder result
IRESfinder score
0.663742197
IRES/non IRES
IRES
riboCIRC information
riboCIRC ID
NA
NA
Evidence
Peptide sequence:
NA
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