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mmu_circRbfox2_727
Basic information of circular RNA
PanCircBase ID:
mmu_circRbfox2_727
mm39_Chr. Position ID:
chr15|76983439|77017141|-
Gene name:
Rbfox2
Transcript:
ENSMUST00000171751.10
CircRNA type:
Exonic circular (circ)RNA
Exon/Intron count:
7
Exon/intron indexes:
9,8,7,6,5,4,3
Exon/intron offsets:
0,199,3639,6337,14365,17681,33477
Genomic length:
33702
Exon/intron sizes in nt:
9,35,46,19,35,41,47,220
Flanking exon/introns:
chr15:76982284-76983439|chr15:77017141-77115586
Splice length:
727
Other database IDs:
Human Ortholog IDs:
Mature spliced Sequence:
GGTAACCAGGAGCCAACAACAACTCCTGACGCAATGGTTCAGCCTTTTACTACCATCCCGTTCCCACCACCTCCACAAAATGGAATTCCCACAGAATATGGAGTGCCACACACTCAGGACTATGCCGGCCAGACCAGTGAACATAACCTGACCCTCTACGGGAGTACGCAGCCTCATGGAGAACAGAGTAGCAATTCACCCAGCAACCAGAATGGATCTCTCACGCAGACAGAAGGTGGAGCACAGACAGACGGACAACAGTCACAGACACAAAGTAGTGAAAATTCAGAGAGTAAATCTACGCCCAAGCGACTACATGTCTCTAATATTCCCTTCCGCTTCCGAGACCCTGACCTCCGGCAGATGTTTGGGCAGTTTGGCAAAATCCTAGATGTGGAAATAATCTTTAATGAGCGCGGCTCCAAGGGATTCGGGTTCGTAACTTTCGAGAATAGTGCTGATGCAGACAGGGCCAGGGAGAAATTGCACGGCACCGTGGTAGAGGGCCGTAAAATCGAGGTGAATAATGCAACAGCACGGGTCATGACCAACAAGAAGATGGTCACGCCATATGCAAATGGCTGGAAGTTAAGCCCAGTAGTTGGAGCTGTGTATGGTCCTGAGTTATATGCAGCATCCAGCTTTCAAGCTGATGTGTCCCTAGGCAATGAGGCGGCTGTGCCCTTGTCAGGAAGAGGAGGCATCAACACTTACATCCCTCTAATCA
Divergent primers for circular RNA PCR
Primer Set-1
Forward primer
Tm
Reverse primer
Tm
Product size
GCTGATGTGTCCCTAGGCAA
59.75
TTTGTGGAGGTGGTGGGAAC
60.11
158
Primer Set-2
Forward primer
Tm
Reverse primer
Tm
Product size
GTGTCCCTAGGCAATGAGGC
60.46
TTTGTGGAGGTGGTGGGAAC
60.11
152
PCR template sequence:
TATGCAGCATCCAGCTTTCAAGCTGATGTGTCCCTAGGCAATGAGGCGGCTGTGCCCTTGTCAGGAAGAGGAGGCATCAACACTTACATCCCTCTAATCAGGTAACCAGGAGCCAACAACAACTCCTGACGCAATGGTTCAGCCTTTTACTACCATCCCGTTCCCACCACCTCCACAAAATGGAATTCCCACAGAATATG
Note: Users can design additional primers for provided template sequence using Primer3 or NCBI primer-blast.
miRNAs associated with circular RNAs
No of miRNAs
8
Interacting miRNAs (#binding sites)
mmu-miR-134-5p(1), mmu-miR-328-3p(1), mmu-miR-320-3p(1), mmu-miR-339-5p(1), mmu-miR-27a-5p(1), mmu-miR-410-3p(1), mmu-miR-344d-3p(1), mmu-miR-574-5p(1)
siRNAs for circular RNA silencing
Junction sequence
ATCCCTCTAATCAGGTAACCAGGAGC
siRNA sets
NA
Protein-coding potential of circular RNAs
CPAT analysis
CPAT ORF ID
CPAT Fickett
CPAT Hexamer
Coding probabilty
ORF length
CIRCRBFOX2_727_ORF_1
0.8564
0.259910748
0.918516508
699
ORF sequence:
ATGGTTCAGCCTTTTACTACCATCCCGTTCCCACCACCTCCACAAAATGGAATTCCCACAGAATATGGAGTGCCACACACTCAGGACTATGCCGGCCAGACCAGTGAACATAACCTGACCCTCTACGGGAGTACGCAGCCTCATGGAGAACAGAGTAGCAATTCACCCAGCAACCAGAATGGATCTCTCACGCAGACAGAAGGTGGAGCACAGACAGACGGACAACAGTCACAGACACAAAGTAGTGAAAATTCAGAGAGTAAATCTACGCCCAAGCGACTACATGTCTCTAATATTCCCTTCCGCTTCCGAGACCCTGACCTCCGGCAGATGTTTGGGCAGTTTGGCAAAATCCTAGATGTGGAAATAATCTTTAATGAGCGCGGCTCCAAGGGATTCGGGTTCGTAACTTTCGAGAATAGTGCTGATGCAGACAGGGCCAGGGAGAAATTGCACGGCACCGTGGTAGAGGGCCGTAAAATCGAGGTGAATAATGCAACAGCACGGGTCATGACCAACAAGAAGATGGTCACGCCATATGCAAATGGCTGGAAGTTAAGCCCAGTAGTTGGAGCTGTGTATGGTCCTGAGTTATATGCAGCATCCAGCTTTCAAGCTGATGTGTCCCTAGGCAATGAGGCGGCTGTGCCCTTGTCAGGAAGAGGAGGCATCAACACTTACATCCCTCTAATCAGGTAA
Peptide sequence:
MVQPFTTIPFPPPPQNGIPTEYGVPHTQDYAGQTSEHNLTLYGSTQPHGEQSSNSPSNQNGSLTQTEGGAQTDGQQSQTQSSENSESKSTPKRLHVSNIPFRFRDPDLRQMFGQFGKILDVEIIFNERGSKGFGFVTFENSADADRAREKLHGTVVEGRKIEVNNATARVMTNKKMVTPYANGWKLSPVVGAVYGPELYAASSFQADVSLGNEAAVPLSGRGGINTYIPLIR
IRESfinder result
IRESfinder score
0.409108234
IRES/non IRES
non-IRES
riboCIRC information
riboCIRC ID
NA
NA
Evidence
Peptide sequence:
NA
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