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mmu_circCopa_848
Basic information of circular RNA
PanCircBase ID:
mmu_circCopa_848
mm39_Chr. Position ID:
chr1|171918505|171931826|+
Gene name:
Copa
Transcript:
ENSMUST00000135192.8
CircRNA type:
Exonic circular (circ)RNA
Exon/Intron count:
8
Exon/intron indexes:
4,5,6,7,8,9,10,11
Exon/intron offsets:
0,225,1306,6735,8729,10440,11271,13170
Genomic length:
13321
Exon/intron sizes in nt:
81,77,11,01,10,10,01,30,00,000
Flanking exon/introns:
chr1:171916737-171918505|chr1:171931826-171932752
Splice length:
848
Other database IDs:
Human Ortholog IDs:
Mature spliced Sequence:
GTTTGGAATTACAAACTTCGGCGCTGCCTGTTCACATTGCTCGGGCACTTGGATTATATCCGTACAACGTTTTTCCATCATGAATATCCTTGGATTCTGAGCGCCTCAGATGATCAGACCATTCGGGTGTGGAACTGGCAGTCTAGAACCTGTGTCTGTGTGTTAACGGGGCACAACCATTATGTAATGTGTGCTCAGTTCCACCCCTCTGAAGACCTGGTGGTATCAGCTAGCCTGGACCAGACTGTCCGCGTTTGGGATATTTCTGGTCTAAGGAAGAAAAACTTGTCTCCTGGTGCGGTGGAGTCGGATGTGAGAGGAATAACTGGCGTTGATCTGTTTGGAACCACGGATGCCGTGGTGAAGCATGTGCTAGAGGGTCATGACCGTGGAGTCAACTGGGCTGCCTTCCACCCGACTATGCCCCTTATTGTATCTGGGGCAGATGACCGGCAAGTGAAGATCTGGCGTATGAATGAATCAAAGGCATGGGAGGTTGACACCTGCCGGGGCCATTACAACAATGTGTCTTGTGCTGTTTTTCACCCTCGCCAAGAGTTGATCCTCAGCAATTCTGAAGACAAGAGTATTCGAGTCTGGGATATGTCTAAGCGGACTGGGGTTCAGACTTTCCGTAGGGATCATGATCGCTTCTGGGTCCTGGCTGCCCATCCCAACCTTAACCTCTTTGCAGCAGGCCATGATGGTGGGATGATTGTATTTAAGCTGGAACGTGAGCGTCCTGCCTATGCTGTTCATGGTAACATGCTGCATTATGTAAAGGACCGATTCCTCCGTCAGCTGGATTTCAACAGCTCCAAAGATGTAGCTGTGATGCAGTTGCGGAG
Divergent primers for circular RNA PCR
Primer Set-1
Forward primer
Tm
Reverse primer
Tm
Product size
TGCTGCATTATGTAAAGGACCG
59.06
TATAATCCAAGTGCCCGAGC
57.46
140
Primer Set-2
Forward primer
Tm
Reverse primer
Tm
Product size
TGCTGCATTATGTAAAGGACCGA
60.37
TATAATCCAAGTGCCCGAGC
57.46
140
PCR template sequence:
ATGCTGTTCATGGTAACATGCTGCATTATGTAAAGGACCGATTCCTCCGTCAGCTGGATTTCAACAGCTCCAAAGATGTAGCTGTGATGCAGTTGCGGAGGTTTGGAATTACAAACTTCGGCGCTGCCTGTTCACATTGCTCGGGCACTTGGATTATATCCGTACAACGTTTTTCCATCATGAATATCCTTGGATTCTGA
Note: Users can design additional primers for provided template sequence using Primer3 or NCBI primer-blast.
miRNAs associated with circular RNAs
No of miRNAs
7
Interacting miRNAs (#binding sites)
mmu-miR-103-3p(1), mmu-miR-217-5p(1), mmu-miR-222-3p(1), mmu-miR-433-3p(1), mmu-miR-107-3p(1), mmu-miR-673-5p(1), mmu-miR-323-3p(1)
siRNAs for circular RNA silencing
Junction sequence
TGCAGTTGCGGAGGTTTGGAATTACA
siRNA sets
TGTAATTCCAAACCTCCGC, AATTCCAAACCTCCGCAAC, ATTCCAAACCTCCGCAACT
Protein-coding potential of circular RNAs
CPAT analysis
CPAT ORF ID
CPAT Fickett
CPAT Hexamer
Coding probabilty
ORF length
CIRCCOPA_848_ORF_1
1.0457
0.190115771
0.949694412
762
ORF sequence:
ATGTGTGCTCAGTTCCACCCCTCTGAAGACCTGGTGGTATCAGCTAGCCTGGACCAGACTGTCCGCGTTTGGGATATTTCTGGTCTAAGGAAGAAAAACTTGTCTCCTGGTGCGGTGGAGTCGGATGTGAGAGGAATAACTGGCGTTGATCTGTTTGGAACCACGGATGCCGTGGTGAAGCATGTGCTAGAGGGTCATGACCGTGGAGTCAACTGGGCTGCCTTCCACCCGACTATGCCCCTTATTGTATCTGGGGCAGATGACCGGCAAGTGAAGATCTGGCGTATGAATGAATCAAAGGCATGGGAGGTTGACACCTGCCGGGGCCATTACAACAATGTGTCTTGTGCTGTTTTTCACCCTCGCCAAGAGTTGATCCTCAGCAATTCTGAAGACAAGAGTATTCGAGTCTGGGATATGTCTAAGCGGACTGGGGTTCAGACTTTCCGTAGGGATCATGATCGCTTCTGGGTCCTGGCTGCCCATCCCAACCTTAACCTCTTTGCAGCAGGCCATGATGGTGGGATGATTGTATTTAAGCTGGAACGTGAGCGTCCTGCCTATGCTGTTCATGGTAACATGCTGCATTATGTAAAGGACCGATTCCTCCGTCAGCTGGATTTCAACAGCTCCAAAGATGTAGCTGTGATGCAGTTGCGGAGGTTTGGAATTACAAACTTCGGCGCTGCCTGTTCACATTGCTCGGGCACTTGGATTATATCCGTACAACGTTTTTCCATCATGAATATCCTTGGATTCTGA
Peptide sequence:
MCAQFHPSEDLVVSASLDQTVRVWDISGLRKKNLSPGAVESDVRGITGVDLFGTTDAVVKHVLEGHDRGVNWAAFHPTMPLIVSGADDRQVKIWRMNESKAWEVDTCRGHYNNVSCAVFHPRQELILSNSEDKSIRVWDMSKRTGVQTFRRDHDRFWVLAAHPNLNLFAAGHDGGMIVFKLERERPAYAVHGNMLHYVKDRFLRQLDFNSSKDVAVMQLRRFGITNFGAACSHCSGTWIISVQRFSIMNILGF
IRESfinder result
IRESfinder score
0.424217689
IRES/non IRES
non-IRES
riboCIRC information
riboCIRC ID
NA
NA
Evidence
Peptide sequence:
NA
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