top of page
mmu_circCopa_452
Basic information of circular RNA
PanCircBase ID:
mmu_circCopa_452
mm39_Chr. Position ID:
chr1|171916663|171925350|+
Gene name:
Copa
Transcript:
ENSMUST00000135192.8
CircRNA type:
Exonic circular (circ)RNA
Exon/Intron count:
5
Exon/intron indexes:
3,4,5,6,7
Exon/intron offsets:
0,1842,2067,3148,8577
Genomic length:
8687
Exon/intron sizes in nt:
7,48,17,71,10,110
Flanking exon/introns:
chr1:171915232-171916663|chr1:171925350-171927234
Splice length:
452
Other database IDs:
CIRCpedia: MMU_CIRCpedia_11840, circAtlas: mmu-Copa_0021
Human Ortholog IDs:
Mature spliced Sequence:
GTCCAGTGCGTGGCATTGACTTCCATAAGCAGCAGCCACTGTTCGTCTCTGGAGGCGATGATTATAAGATTAAGGTTTGGAATTACAAACTTCGGCGCTGCCTGTTCACATTGCTCGGGCACTTGGATTATATCCGTACAACGTTTTTCCATCATGAATATCCTTGGATTCTGAGCGCCTCAGATGATCAGACCATTCGGGTGTGGAACTGGCAGTCTAGAACCTGTGTCTGTGTGTTAACGGGGCACAACCATTATGTAATGTGTGCTCAGTTCCACCCCTCTGAAGACCTGGTGGTATCAGCTAGCCTGGACCAGACTGTCCGCGTTTGGGATATTTCTGGTCTAAGGAAGAAAAACTTGTCTCCTGGTGCGGTGGAGTCGGATGTGAGAGGAATAACTGGCGTTGATCTGTTTGGAACCACGGATGCCGTGGTGAAGCATGTGCTAGAG
Divergent primers for circular RNA PCR
Primer Set-1
Forward primer
Tm
Reverse primer
Tm
Product size
TGGAGTCGGATGTGAGAGGA
59.67
AATCATCGCCTCCAGAGACG
59.61
140
Primer Set-2
Forward primer
Tm
Reverse primer
Tm
Product size
AAACTTGTCTCCTGGTGCGG
60.54
CCTCCAGAGACGAACAGTGG
59.76
152
PCR template sequence:
GAAAAACTTGTCTCCTGGTGCGGTGGAGTCGGATGTGAGAGGAATAACTGGCGTTGATCTGTTTGGAACCACGGATGCCGTGGTGAAGCATGTGCTAGAGGTCCAGTGCGTGGCATTGACTTCCATAAGCAGCAGCCACTGTTCGTCTCTGGAGGCGATGATTATAAGATTAAGGTTTGGAATTACAAACTTCGGCGCTG
Note: Users can design additional primers for provided template sequence using Primer3 or NCBI primer-blast.
miRNAs associated with circular RNAs
No of miRNAs
3
Interacting miRNAs (#binding sites)
mmu-miR-433-3p(1), mmu-miR-3105-3p(1), mmu-miR-323-3p(1)
siRNAs for circular RNA silencing
Junction sequence
GCATGTGCTAGAGGTCCAGTGCGTGG
siRNA sets
NA
Protein-coding potential of circular RNAs
CPAT analysis
CPAT ORF ID
CPAT Fickett
CPAT Hexamer
Coding probabilty
ORF length
CIRCCOPA_452_ORF_1
0.8669
0.052794538
0.311075177
366
ORF sequence:
ATGTGTGCTCAGTTCCACCCCTCTGAAGACCTGGTGGTATCAGCTAGCCTGGACCAGACTGTCCGCGTTTGGGATATTTCTGGTCTAAGGAAGAAAAACTTGTCTCCTGGTGCGGTGGAGTCGGATGTGAGAGGAATAACTGGCGTTGATCTGTTTGGAACCACGGATGCCGTGGTGAAGCATGTGCTAGAGGTCCAGTGCGTGGCATTGACTTCCATAAGCAGCAGCCACTGTTCGTCTCTGGAGGCGATGATTATAAGATTAAGGTTTGGAATTACAAACTTCGGCGCTGCCTGTTCACATTGCTCGGGCACTTGGATTATATCCGTACAACGTTTTTCCATCATGAATATCCTTGGATTCTGA
Peptide sequence:
MCAQFHPSEDLVVSASLDQTVRVWDISGLRKKNLSPGAVESDVRGITGVDLFGTTDAVVKHVLEVQCVALTSISSSHCSSLEAMIIRLRFGITNFGAACSHCSGTWIISVQRFSIMNILGF
IRESfinder result
IRESfinder score
0.519642171
IRES/non IRES
IRES
riboCIRC information
riboCIRC ID
NA
NA
Evidence
Peptide sequence:
NA
bottom of page