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mmu_circEpb41_306
Basic information of circular RNA
PanCircBase ID:
mmu_circEpb41_306
mm39_Chr. Position ID:
chr4|131663049|131685130|-
Gene name:
Epb41
Transcript:
ENSMUST00000146443.8
CircRNA type:
Exonic circular (circ)RNA
Exon/Intron count:
2
Exon/intron indexes:
5,4
Exon/intron offsets:
0,21904
Genomic length:
22081
Exon/intron sizes in nt:
129,177
Flanking exon/introns:
chr4:131657106-131663049|chr4:131685130-131690234
Splice length:
306
Other database IDs:
circAtlas: mmu-Epb4_0040
circAtlas: hsa-EPB41_0020, CIRCpedia: HSA_CIRCpedia_31270
Human Ortholog IDs:
Mature spliced Sequence:
GATTTAGACAAGAGTCAAGAAGAGATCAAAAAGCACCATGCCAGCATCAGTGAACTGAAAAAGAACTTTATGGAATCGGTACCCGAACCACGGCCCAGCGAGTGGGACAAGCGCTTATCTACACACTCACCCTTCCGGACTCTTAACATCAACGGGCAAGTCCCTACTGGAGATGGACCTCCTCTGGTAAAGACTCAAACTGTCACCATCTCAGATACTGCCAATGCTGTGAAAAGTGAAATCCCAACCAAAGATGTCCCTATTGTCCACACTGAGACCAAGACCATCACCTATGAAGCTGCCCAG
Divergent primers for circular RNA PCR
Primer Set-1
Forward primer
Tm
Reverse primer
Tm
Product size
TGCCAATGCTGTGAAAAGTGA
58.97
TTCACTGATGCTGGCATGGT
59.96
142
Primer Set-2
Forward primer
Tm
Reverse primer
Tm
Product size
ACTGCCAATGCTGTGAAAAGT
58.97
TTCACTGATGCTGGCATGGT
59.96
144
PCR template sequence:
CATCTCAGATACTGCCAATGCTGTGAAAAGTGAAATCCCAACCAAAGATGTCCCTATTGTCCACACTGAGACCAAGACCATCACCTATGAAGCTGCCCAGGATTTAGACAAGAGTCAAGAAGAGATCAAAAAGCACCATGCCAGCATCAGTGAACTGAAAAAGAACTTTATGGAATCGGTACCCGAACCACGGCCCAGCG
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-9-5p(1), mmu-miR-34a-5p(1), mmu-miR-298-5p(1), mmu-miR-673-5p(1), mmu-miR-574-5p(1)
siRNAs for circular RNA silencing
Junction sequence
TGAAGCTGCCCAGGATTTAGACAAGA
siRNA sets
TAAATCCTGGGCAGCTTCA, CTAAATCCTGGGCAGCTTC
Protein-coding potential of circular RNAs
CPAT analysis
CPAT ORF ID
CPAT Fickett
CPAT Hexamer
Coding probabilty
ORF length
CIRCEPB41_306_ORF_1
1.1149
0.373319281
0.905569326
543
ORF sequence:
ATGGAATCGGTACCCGAACCACGGCCCAGCGAGTGGGACAAGCGCTTATCTACACACTCACCCTTCCGGACTCTTAACATCAACGGGCAAGTCCCTACTGGAGATGGACCTCCTCTGGTAAAGACTCAAACTGTCACCATCTCAGATACTGCCAATGCTGTGAAAAGTGAAATCCCAACCAAAGATGTCCCTATTGTCCACACTGAGACCAAGACCATCACCTATGAAGCTGCCCAGGATTTAGACAAGAGTCAAGAAGAGATCAAAAAGCACCATGCCAGCATCAGTGAACTGAAAAAGAACTTTATGGAATCGGTACCCGAACCACGGCCCAGCGAGTGGGACAAGCGCTTATCTACACACTCACCCTTCCGGACTCTTAACATCAACGGGCAAGTCCCTACTGGAGATGGACCTCCTCTGGTAAAGACTCAAACTGTCACCATCTCAGATACTGCCAATGCTGTGAAAAGTGAAATCCCAACCAAAGATGTCCCTATTGTCCACACTGAGACCAAGACCATCACCTATGAAGCTGCCCAG
Peptide sequence:
MESVPEPRPSEWDKRLSTHSPFRTLNINGQVPTGDGPPLVKTQTVTISDTANAVKSEIPTKDVPIVHTETKTITYEAAQDLDKSQEEIKKHHASISELKKNFMESVPEPRPSEWDKRLSTHSPFRTLNINGQVPTGDGPPLVKTQTVTISDTANAVKSEIPTKDVPIVHTETKTITYEAAQ
IRESfinder result
IRESfinder score
0.389204521
IRES/non IRES
non-IRES
riboCIRC information
riboCIRC ID
NA
NA
Evidence
Peptide sequence:
NA
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