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mmu_circMdm4_519
Basic information of circular RNA
PanCircBase ID:
mmu_circMdm4_519
mm39_Chr. Position ID:
chr1|132929020|132938936|-
Gene name:
Mdm4
Transcript:
ENSMUST00000186617.7
CircRNA type:
Exonic circular (circ)RNA
Exon/Intron count:
5
Exon/intron indexes:
8,7,6,5,4
Exon/intron offsets:
0,2508,3371,7854,9782
Genomic length:
9916
Exon/intron sizes in nt:
16,11,00,68,56,134
Flanking exon/introns:
chr1:132924447-132929020|chr1:132938936-132940374
Splice length:
519
Other database IDs:
circAtlas: hsa-SCAF8_0001, CIRCpedia: HSA_CIRCpedia_160062
Human Ortholog IDs:
Mature spliced Sequence:
GTAATGCACTATCTAGGCCAGTATATAATGGTGAAGCAGCTCTATGATCAACAGGAGCAACATATGGTATACTGTGGTGGAGATCTTTTGGGAGATCTACTTGGATGTCAGAGCTTTTCTGTGAAAGATCCAAGCCCTCTCTATGACATGCTAAGAAAGAATCTTGTTACATCAGCTTCTATTAACACAGATGCTGCTCAGACTCTCGCTCTCGCACAGGATCACACTATGGATTTTCCAAGTCAAGACCGACTGAAGCACGGTGCAACAGAATACTCCAATCCCAGAAAAAGAACTGAAGAAGAGGATACTCACACACTGCCTACCTCACGACATAAATGCAGAGACTCCAGAGCAGATGAAGACTTGATAGAACATTTATCTCAAGATGAGACATCTAGGCTTGACCTTGATTTTGAGGAGTGGGACGTTGCTGGCCTGCCTTGGTGGTTTCTAGGGAATTTGAGAAACAACTGTATTCCTAAAAGTAATGGCTCAACTGATTTACAGACAAATCAG
Divergent primers for circular RNA PCR
Primer Set-1
Forward primer
Tm
Reverse primer
Tm
Product size
GCCTGCCTTGGTGGTTTCTA
60.25
TCCCAAAAGATCTCCACCACAG
59.96
176
Primer Set-2
Forward primer
Tm
Reverse primer
Tm
Product size
GCCTGCCTTGGTGGTTTCTA
60.25
CTCCCAAAAGATCTCCACCACA
59.96
177
PCR template sequence:
GGAGTGGGACGTTGCTGGCCTGCCTTGGTGGTTTCTAGGGAATTTGAGAAACAACTGTATTCCTAAAAGTAATGGCTCAACTGATTTACAGACAAATCAGGTAATGCACTATCTAGGCCAGTATATAATGGTGAAGCAGCTCTATGATCAACAGGAGCAACATATGGTATACTGTGGTGGAGATCTTTTGGGAGATCTAC
Note: Users can design additional primers for provided template sequence using Primer3 or NCBI primer-blast.
miRNAs associated with circular RNAs
No of miRNAs
10
Interacting miRNAs (#binding sites)
mmu-let-7a-5p(1), mmu-let-7e-5p(1), mmu-let-7b-5p(1), mmu-miR-34c-5p(1), mmu-miR-34a-5p(1), mmu-let-7c-5p(1), mmu-miR-322-5p(1), mmu-miR-411-3p(1), mmu-miR-98-5p(1), mmu-miR-193b-3p(1)
siRNAs for circular RNA silencing
Junction sequence
ACAGACAAATCAGGTAATGCACTATC
siRNA sets
AGTGCATTACCTGATTTGT, GTGCATTACCTGATTTGTC, TAGTGCATTACCTGATTTG
Protein-coding potential of circular RNAs
CPAT analysis
CPAT ORF ID
CPAT Fickett
CPAT Hexamer
Coding probabilty
ORF length
CIRCMDM4_519_ORF_1
1.0567
0.024992218
0.98619474
1035
ORF sequence:
ATGCACTATCTAGGCCAGTATATAATGGTGAAGCAGCTCTATGATCAACAGGAGCAACATATGGTATACTGTGGTGGAGATCTTTTGGGAGATCTACTTGGATGTCAGAGCTTTTCTGTGAAAGATCCAAGCCCTCTCTATGACATGCTAAGAAAGAATCTTGTTACATCAGCTTCTATTAACACAGATGCTGCTCAGACTCTCGCTCTCGCACAGGATCACACTATGGATTTTCCAAGTCAAGACCGACTGAAGCACGGTGCAACAGAATACTCCAATCCCAGAAAAAGAACTGAAGAAGAGGATACTCACACACTGCCTACCTCACGACATAAATGCAGAGACTCCAGAGCAGATGAAGACTTGATAGAACATTTATCTCAAGATGAGACATCTAGGCTTGACCTTGATTTTGAGGAGTGGGACGTTGCTGGCCTGCCTTGGTGGTTTCTAGGGAATTTGAGAAACAACTGTATTCCTAAAAGTAATGGCTCAACTGATTTACAGACAAATCAGGTAATGCACTATCTAGGCCAGTATATAATGGTGAAGCAGCTCTATGATCAACAGGAGCAACATATGGTATACTGTGGTGGAGATCTTTTGGGAGATCTACTTGGATGTCAGAGCTTTTCTGTGAAAGATCCAAGCCCTCTCTATGACATGCTAAGAAAGAATCTTGTTACATCAGCTTCTATTAACACAGATGCTGCTCAGACTCTCGCTCTCGCACAGGATCACACTATGGATTTTCCAAGTCAAGACCGACTGAAGCACGGTGCAACAGAATACTCCAATCCCAGAAAAAGAACTGAAGAAGAGGATACTCACACACTGCCTACCTCACGACATAAATGCAGAGACTCCAGAGCAGATGAAGACTTGATAGAACATTTATCTCAAGATGAGACATCTAGGCTTGACCTTGATTTTGAGGAGTGGGACGTTGCTGGCCTGCCTTGGTGGTTTCTAGGGAATTTGAGAAACAACTGTATTCCTAAAAGTAATGGCTCAACTGATTTACAGACAAATCAG
Peptide sequence:
MHYLGQYIMVKQLYDQQEQHMVYCGGDLLGDLLGCQSFSVKDPSPLYDMLRKNLVTSASINTDAAQTLALAQDHTMDFPSQDRLKHGATEYSNPRKRTEEEDTHTLPTSRHKCRDSRADEDLIEHLSQDETSRLDLDFEEWDVAGLPWWFLGNLRNNCIPKSNGSTDLQTNQVMHYLGQYIMVKQLYDQQEQHMVYCGGDLLGDLLGCQSFSVKDPSPLYDMLRKNLVTSASINTDAAQTLALAQDHTMDFPSQDRLKHGATEYSNPRKRTEEEDTHTLPTSRHKCRDSRADEDLIEHLSQDETSRLDLDFEEWDVAGLPWWFLGNLRNNCIPKSNGSTDLQTNQ
IRESfinder result
IRESfinder score
0.637945924
IRES/non IRES
IRES
riboCIRC information
riboCIRC ID
NA
NA
Evidence
Peptide sequence:
NA
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