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mmu_circCopa_806
Basic information of circular RNA
PanCircBase ID:
mmu_circCopa_806
mm39_Chr. Position ID:
chr1|171925240|171935961|+
Gene name:
Copa
Transcript:
ENSMUST00000135192.8
CircRNA type:
Exonic circular (circ)RNA
Exon/Intron count:
8
Exon/intron indexes:
7,8,9,10,11,12,13,14
Exon/intron offsets:
0,1994,3705,4536,6435,7512,8443,10638
Genomic length:
10721
Exon/intron sizes in nt:
110,100,136,83,151,67,76,83
Flanking exon/introns:
chr1:171919921-171925240|chr1:171935961-171937352
Splice length:
806
Other database IDs:
Human Ortholog IDs:
Mature spliced Sequence:
GTCTAAGGAAGAAAAACTTGTCTCCTGGTGCGGTGGAGTCGGATGTGAGAGGAATAACTGGCGTTGATCTGTTTGGAACCACGGATGCCGTGGTGAAGCATGTGCTAGAGGGTCATGACCGTGGAGTCAACTGGGCTGCCTTCCACCCGACTATGCCCCTTATTGTATCTGGGGCAGATGACCGGCAAGTGAAGATCTGGCGTATGAATGAATCAAAGGCATGGGAGGTTGACACCTGCCGGGGCCATTACAACAATGTGTCTTGTGCTGTTTTTCACCCTCGCCAAGAGTTGATCCTCAGCAATTCTGAAGACAAGAGTATTCGAGTCTGGGATATGTCTAAGCGGACTGGGGTTCAGACTTTCCGTAGGGATCATGATCGCTTCTGGGTCCTGGCTGCCCATCCCAACCTTAACCTCTTTGCAGCAGGCCATGATGGTGGGATGATTGTATTTAAGCTGGAACGTGAGCGTCCTGCCTATGCTGTTCATGGTAACATGCTGCATTATGTAAAGGACCGATTCCTCCGTCAGCTGGATTTCAACAGCTCCAAAGATGTAGCTGTGATGCAGTTGCGGAGCGGTTCTAAGTTTCCAGTATTCAACATGTCATACAATCCAGCAGAAAACGCAGTGCTGCTCTGCACCAGAGCAAGCAATCTAGAGAACAGTACCTACGACCTATACACCATCCCCAAAGACGCAGACTCCCAGAACCCTGACGCCCCTGAAGGGAAACGATCCTCAGGCCTGACAGCGGTTTGGGTTGCTCGGAATCGGTTTGCTGTCCTAGATCGCATGCATTCA
Divergent primers for circular RNA PCR
Primer Set-1
Forward primer
Tm
Reverse primer
Tm
Product size
AAACGATCCTCAGGCCTGAC
59.75
GCATCCGTGGTTCCAAACAG
59.76
160
Primer Set-2
Forward primer
Tm
Reverse primer
Tm
Product size
GGAAACGATCCTCAGGCCTG
60.46
GCATCCGTGGTTCCAAACAG
59.76
162
PCR template sequence:
CTCCCAGAACCCTGACGCCCCTGAAGGGAAACGATCCTCAGGCCTGACAGCGGTTTGGGTTGCTCGGAATCGGTTTGCTGTCCTAGATCGCATGCATTCAGTCTAAGGAAGAAAAACTTGTCTCCTGGTGCGGTGGAGTCGGATGTGAGAGGAATAACTGGCGTTGATCTGTTTGGAACCACGGATGCCGTGGTGAAGCA
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-103-3p(1), mmu-miR-322-5p(1), mmu-miR-15b-5p(1), mmu-miR-217-5p(1), mmu-miR-222-3p(1), mmu-miR-107-3p(1), mmu-miR-190b-5p(1), mmu-miR-673-5p(1)
siRNAs for circular RNA silencing
Junction sequence
TCGCATGCATTCAGTCTAAGGAAGAA
siRNA sets
CTTAGACTGAATGCATGCG, CTTCCTTAGACTGAATGCA, TTCCTTAGACTGAATGCAT
Protein-coding potential of circular RNAs
CPAT analysis
CPAT ORF ID
CPAT Fickett
CPAT Hexamer
Coding probabilty
ORF length
CIRCCOPA_806_ORF_1
0.9891
0.251499354
0.912904612
660
ORF sequence:
ATGCCCCTTATTGTATCTGGGGCAGATGACCGGCAAGTGAAGATCTGGCGTATGAATGAATCAAAGGCATGGGAGGTTGACACCTGCCGGGGCCATTACAACAATGTGTCTTGTGCTGTTTTTCACCCTCGCCAAGAGTTGATCCTCAGCAATTCTGAAGACAAGAGTATTCGAGTCTGGGATATGTCTAAGCGGACTGGGGTTCAGACTTTCCGTAGGGATCATGATCGCTTCTGGGTCCTGGCTGCCCATCCCAACCTTAACCTCTTTGCAGCAGGCCATGATGGTGGGATGATTGTATTTAAGCTGGAACGTGAGCGTCCTGCCTATGCTGTTCATGGTAACATGCTGCATTATGTAAAGGACCGATTCCTCCGTCAGCTGGATTTCAACAGCTCCAAAGATGTAGCTGTGATGCAGTTGCGGAGCGGTTCTAAGTTTCCAGTATTCAACATGTCATACAATCCAGCAGAAAACGCAGTGCTGCTCTGCACCAGAGCAAGCAATCTAGAGAACAGTACCTACGACCTATACACCATCCCCAAAGACGCAGACTCCCAGAACCCTGACGCCCCTGAAGGGAAACGATCCTCAGGCCTGACAGCGGTTTGGGTTGCTCGGAATCGGTTTGCTGTCCTAGATCGCATGCATTCAGTCTAA
Peptide sequence:
MPLIVSGADDRQVKIWRMNESKAWEVDTCRGHYNNVSCAVFHPRQELILSNSEDKSIRVWDMSKRTGVQTFRRDHDRFWVLAAHPNLNLFAAGHDGGMIVFKLERERPAYAVHGNMLHYVKDRFLRQLDFNSSKDVAVMQLRSGSKFPVFNMSYNPAENAVLLCTRASNLENSTYDLYTIPKDADSQNPDAPEGKRSSGLTAVWVARNRFAVLDRMHSV
IRESfinder result
IRESfinder score
0.319255577
IRES/non IRES
non-IRES
riboCIRC information
riboCIRC ID
NA
NA
Evidence
Peptide sequence:
NA
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