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mmu_circCopa_833
Basic information of circular RNA
PanCircBase ID:
mmu_circCopa_833
mm39_Chr. Position ID:
chr1|171919811|171933759|+
Gene name:
Copa
Transcript:
ENSMUST00000135192.8
CircRNA type:
Exonic circular (circ)RNA
Exon/Intron count:
8
Exon/intron indexes:
6,7,8,9,10,11,12,13
Exon/intron offsets:
0,5429,7423,9134,9965,11864,12941,13872
Genomic length:
13948
Exon/intron sizes in nt:
110,110,100,136,83,151,67,76
Flanking exon/introns:
chr1:171918807-171919811|chr1:171933759-171935878
Splice length:
833
Other database IDs:
circAtlas: hsa-SCAF8_0001, CIRCpedia: HSA_CIRCpedia_109894
Human Ortholog IDs:
Mature spliced Sequence:
TGTGTTAACGGGGCACAACCATTATGTAATGTGTGCTCAGTTCCACCCCTCTGAAGACCTGGTGGTATCAGCTAGCCTGGACCAGACTGTCCGCGTTTGGGATATTTCTGGTCTAAGGAAGAAAAACTTGTCTCCTGGTGCGGTGGAGTCGGATGTGAGAGGAATAACTGGCGTTGATCTGTTTGGAACCACGGATGCCGTGGTGAAGCATGTGCTAGAGGGTCATGACCGTGGAGTCAACTGGGCTGCCTTCCACCCGACTATGCCCCTTATTGTATCTGGGGCAGATGACCGGCAAGTGAAGATCTGGCGTATGAATGAATCAAAGGCATGGGAGGTTGACACCTGCCGGGGCCATTACAACAATGTGTCTTGTGCTGTTTTTCACCCTCGCCAAGAGTTGATCCTCAGCAATTCTGAAGACAAGAGTATTCGAGTCTGGGATATGTCTAAGCGGACTGGGGTTCAGACTTTCCGTAGGGATCATGATCGCTTCTGGGTCCTGGCTGCCCATCCCAACCTTAACCTCTTTGCAGCAGGCCATGATGGTGGGATGATTGTATTTAAGCTGGAACGTGAGCGTCCTGCCTATGCTGTTCATGGTAACATGCTGCATTATGTAAAGGACCGATTCCTCCGTCAGCTGGATTTCAACAGCTCCAAAGATGTAGCTGTGATGCAGTTGCGGAGCGGTTCTAAGTTTCCAGTATTCAACATGTCATACAATCCAGCAGAAAACGCAGTGCTGCTCTGCACCAGAGCAAGCAATCTAGAGAACAGTACCTACGACCTATACACCATCCCCAAAGACGCAGACTCCCAGAACCCTGACG
Divergent primers for circular RNA PCR
Primer Set-1
Forward primer
Tm
Reverse primer
Tm
Product size
CTGCACCAGAGCAAGCAATC
59.83
TCTGGTCCAGGCTAGCTGAT
60.03
169
Primer Set-2
Forward primer
Tm
Reverse primer
Tm
Product size
TGCACCAGAGCAAGCAATCT
60.25
TCTGGTCCAGGCTAGCTGAT
60.03
168
PCR template sequence:
GAAAACGCAGTGCTGCTCTGCACCAGAGCAAGCAATCTAGAGAACAGTACCTACGACCTATACACCATCCCCAAAGACGCAGACTCCCAGAACCCTGACGTGTGTTAACGGGGCACAACCATTATGTAATGTGTGCTCAGTTCCACCCCTCTGAAGACCTGGTGGTATCAGCTAGCCTGGACCAGACTGTCCGCGTTTGG
Note: Users can design additional primers for provided template sequence using Primer3 or NCBI primer-blast.
miRNAs associated with circular RNAs
No of miRNAs
9
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), mmu-miR-323-3p(1)
siRNAs for circular RNA silencing
Junction sequence
CAGAACCCTGACGTGTGTTAACGGGG
siRNA sets
NA
Protein-coding potential of circular RNAs
CPAT analysis
CPAT ORF ID
CPAT Fickett
CPAT Hexamer
Coding probabilty
ORF length
CIRCCOPA_833_ORF_1
1.1636
0.249581028
0.977448516
813
ORF sequence:
ATGTGTGCTCAGTTCCACCCCTCTGAAGACCTGGTGGTATCAGCTAGCCTGGACCAGACTGTCCGCGTTTGGGATATTTCTGGTCTAAGGAAGAAAAACTTGTCTCCTGGTGCGGTGGAGTCGGATGTGAGAGGAATAACTGGCGTTGATCTGTTTGGAACCACGGATGCCGTGGTGAAGCATGTGCTAGAGGGTCATGACCGTGGAGTCAACTGGGCTGCCTTCCACCCGACTATGCCCCTTATTGTATCTGGGGCAGATGACCGGCAAGTGAAGATCTGGCGTATGAATGAATCAAAGGCATGGGAGGTTGACACCTGCCGGGGCCATTACAACAATGTGTCTTGTGCTGTTTTTCACCCTCGCCAAGAGTTGATCCTCAGCAATTCTGAAGACAAGAGTATTCGAGTCTGGGATATGTCTAAGCGGACTGGGGTTCAGACTTTCCGTAGGGATCATGATCGCTTCTGGGTCCTGGCTGCCCATCCCAACCTTAACCTCTTTGCAGCAGGCCATGATGGTGGGATGATTGTATTTAAGCTGGAACGTGAGCGTCCTGCCTATGCTGTTCATGGTAACATGCTGCATTATGTAAAGGACCGATTCCTCCGTCAGCTGGATTTCAACAGCTCCAAAGATGTAGCTGTGATGCAGTTGCGGAGCGGTTCTAAGTTTCCAGTATTCAACATGTCATACAATCCAGCAGAAAACGCAGTGCTGCTCTGCACCAGAGCAAGCAATCTAGAGAACAGTACCTACGACCTATACACCATCCCCAAAGACGCAGACTCCCAGAACCCTGACGTGTGTTAA
Peptide sequence:
MCAQFHPSEDLVVSASLDQTVRVWDISGLRKKNLSPGAVESDVRGITGVDLFGTTDAVVKHVLEGHDRGVNWAAFHPTMPLIVSGADDRQVKIWRMNESKAWEVDTCRGHYNNVSCAVFHPRQELILSNSEDKSIRVWDMSKRTGVQTFRRDHDRFWVLAAHPNLNLFAAGHDGGMIVFKLERERPAYAVHGNMLHYVKDRFLRQLDFNSSKDVAVMQLRSGSKFPVFNMSYNPAENAVLLCTRASNLENSTYDLYTIPKDADSQNPDVC
IRESfinder result
IRESfinder score
0.385828137
IRES/non IRES
non-IRES
riboCIRC information
riboCIRC ID
NA
NA
Evidence
Peptide sequence:
NA
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