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mmu_circCox10_453
Basic information of circular RNA
PanCircBase ID:
mmu_circCox10_453
mm39_Chr. Position ID:
chr11|63962343|63964496|-
Gene name:
Cox10
Transcript:
ENSMUST00000049091.9
CircRNA type:
Exonic circular (circ)RNA
Exon/Intron count:
2
Exon/intron indexes:
3,2
Exon/intron offsets:
0,2019
Genomic length:
2153
Exon/intron sizes in nt:
3,19,134
Flanking exon/introns:
chr11:63936177-63962343|chr11:63964496-63970161
Splice length:
453
Other database IDs:
circBase: mmu_circ_0003227, CIRCpedia: MMU_CIRCpedia_25754, circAtlas: mmu-Cox10_0001
circBase: hsa_circ_0007743, circAtlas: hsa-SCAF8_0001, CIRCpedia: HSA_CIRCpedia_19306
Human Ortholog IDs:
Mature spliced Sequence:
GCTCAGTAGGAGGATGTATCTGGTATTTAGAGAGAAGAGCTATACAGGGATTGCCACACAGGGTCACACGTCTGTTCAGGAATGTCAGTAATCAGTGGGTCACGCTCCAGCACTTGAGCTTCCTCAAGCGCATGTATGTCACACAGCTGCACAGGGGCCTTAGCCAGCGAGTCAAACCAAAGCCAGAGCCACCGGCGTCTCCTTTCCTTGAACACACGTCTTCAGGGCAGGCTAGAGCGGACGAGGATGAGCTGCCGTCTTTCCCAGCACCCAGTCGGCCTCTGTCCCGGAAGCCAAATGAGGAGTTGGTGGAGCTGGAGGCGACCTCCATAGTGGACCATTCCCTCGACACAGCCAAAGAGAAAAAGGAAGAAAGGCAGTGGAAAGAGATGAAACTTCACACTGATGATCTGCCTGGCATTTTGGCCAGGCTGTCCAAGATCAAACTCACAG
Divergent primers for circular RNA PCR
Primer Set-1
Forward primer
Tm
Reverse primer
Tm
Product size
ACACTGATGATCTGCCTGGC
60.11
TGACATTCCTGAACAGACGTGT
59.9
141
Primer Set-2
Forward primer
Tm
Reverse primer
Tm
Product size
CACTGATGATCTGCCTGGCA
60.11
TGACATTCCTGAACAGACGTGT
59.9
140
PCR template sequence:
GCCAAAGAGAAAAAGGAAGAAAGGCAGTGGAAAGAGATGAAACTTCACACTGATGATCTGCCTGGCATTTTGGCCAGGCTGTCCAAGATCAAACTCACAGGCTCAGTAGGAGGATGTATCTGGTATTTAGAGAGAAGAGCTATACAGGGATTGCCACACAGGGTCACACGTCTGTTCAGGAATGTCAGTAATCAGTGGGT
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-185-5p(1), mmu-miR-215-5p(1), mmu-miR-29b-2-5p(1), mmu-miR-697(1)
siRNAs for circular RNA silencing
Junction sequence
ATCAAACTCACAGGCTCAGTAGGAGG
siRNA sets
ACTGAGCCTGTGAGTTTGA, CTCCTACTGAGCCTGTGAG
Protein-coding potential of circular RNAs
CPAT analysis
CPAT ORF ID
CPAT Fickett
CPAT Hexamer
Coding probabilty
ORF length
CIRCCOX10_453_ORF_1
1.0408
0.259751159
0.965063792
774
ORF sequence:
ATGTATGTCACACAGCTGCACAGGGGCCTTAGCCAGCGAGTCAAACCAAAGCCAGAGCCACCGGCGTCTCCTTTCCTTGAACACACGTCTTCAGGGCAGGCTAGAGCGGACGAGGATGAGCTGCCGTCTTTCCCAGCACCCAGTCGGCCTCTGTCCCGGAAGCCAAATGAGGAGTTGGTGGAGCTGGAGGCGACCTCCATAGTGGACCATTCCCTCGACACAGCCAAAGAGAAAAAGGAAGAAAGGCAGTGGAAAGAGATGAAACTTCACACTGATGATCTGCCTGGCATTTTGGCCAGGCTGTCCAAGATCAAACTCACAGGCTCAGTAGGAGGATGTATCTGGTATTTAGAGAGAAGAGCTATACAGGGATTGCCACACAGGGTCACACGTCTGTTCAGGAATGTCAGTAATCAGTGGGTCACGCTCCAGCACTTGAGCTTCCTCAAGCGCATGTATGTCACACAGCTGCACAGGGGCCTTAGCCAGCGAGTCAAACCAAAGCCAGAGCCACCGGCGTCTCCTTTCCTTGAACACACGTCTTCAGGGCAGGCTAGAGCGGACGAGGATGAGCTGCCGTCTTTCCCAGCACCCAGTCGGCCTCTGTCCCGGAAGCCAAATGAGGAGTTGGTGGAGCTGGAGGCGACCTCCATAGTGGACCATTCCCTCGACACAGCCAAAGAGAAAAAGGAAGAAAGGCAGTGGAAAGAGATGAAACTTCACACTGATGATCTGCCTGGCATTTTGGCCAGGCTGTCCAAGATCAAACTCACA
Peptide sequence:
MYVTQLHRGLSQRVKPKPEPPASPFLEHTSSGQARADEDELPSFPAPSRPLSRKPNEELVELEATSIVDHSLDTAKEKKEERQWKEMKLHTDDLPGILARLSKIKLTGSVGGCIWYLERRAIQGLPHRVTRLFRNVSNQWVTLQHLSFLKRMYVTQLHRGLSQRVKPKPEPPASPFLEHTSSGQARADEDELPSFPAPSRPLSRKPNEELVELEATSIVDHSLDTAKEKKEERQWKEMKLHTDDLPGILARLSKIKLT
IRESfinder result
IRESfinder score
0.386899055
IRES/non IRES
non-IRES
riboCIRC information
riboCIRC ID
NA
NA
Evidence
Peptide sequence:
NA
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