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mmu_circCopb1_636
Basic information of circular RNA
PanCircBase ID:
mmu_circCopb1_636
mm39_Chr. Position ID:
chr7|113837584|113848212|-
Gene name:
Copb1
Transcript:
ENSMUST00000033012.9
CircRNA type:
Exonic circular (circ)RNA
Exon/Intron count:
5
Exon/intron indexes:
8,7,6,5,4
Exon/intron offsets:
0,2275,7074,8378,10458
Genomic length:
10628
Exon/intron sizes in nt:
120,138,93,115,170
Flanking exon/introns:
chr7:113836869-113837584|chr7:113848212-113849280
Splice length:
636
Other database IDs:
circAtlas: mmu-Copb1_0023
Human Ortholog IDs:
Mature spliced Sequence:
GATCTCCAGCACCCCAATGAGTTTATTCGTGGATCTACTCTTCGTTTCCTTTGCAAATTGAAGGAAGCAGAATTGCTGGAACCTTTAATGCCTGCTATCCGTGCGTGCTTGGAACATCGTCACAGCTATGTTAGGAGAAATGCTGTTTTGGCCATCTATACCATCTACAGAAATTTTGAACATCTTATACCTGATGCTCCTGAACTGATACATGATTTTCTTGTGAATGAGAAGGATGCAAGCTGCAAAAGAAATGCATTTATGATGCTAATTCACGCAGATCAGGATCGAGCTTTGGATTATTTAAGTACATGTATTGATCAAGTTCAGACATTTGGAGACATTCTACAGTTGGTTATTGTTGAACTAATTTATAAGGTCTGTCATGCTAATCCATCAGAAAGGGCCCGCTTCATTCGCTGTATCTATAACTTACTGCAGTCATCTAGTCCTGCTGTAAAATATGAGGCTGCTGGGACACTGGTAACACTGTCAAGTGCACCAACTGCAATAAAGGCTGCTGCTCAGTGTTACATTGATTTAATTATTAAGGAGAGTGATAACAATGTAAAGCTCATCGTCCTGGACCGCTTGGTGGAATTAAAAGAGCATCCTGCTCATGAACGAGTCCTGCAG
Divergent primers for circular RNA PCR
Primer Set-1
Forward primer
Tm
Reverse primer
Tm
Product size
AAAGCTCATCGTCCTGGACC
59.75
GCAGGCATTAAAGGTTCCAGC
60.13
162
Primer Set-2
Forward primer
Tm
Reverse primer
Tm
Product size
AAAGCTCATCGTCCTGGACC
59.75
CAGGCATTAAAGGTTCCAGCA
58.83
161
PCR template sequence:
TGATTTAATTATTAAGGAGAGTGATAACAATGTAAAGCTCATCGTCCTGGACCGCTTGGTGGAATTAAAAGAGCATCCTGCTCATGAACGAGTCCTGCAGGATCTCCAGCACCCCAATGAGTTTATTCGTGGATCTACTCTTCGTTTCCTTTGCAAATTGAAGGAAGCAGAATTGCTGGAACCTTTAATGCCTGCTATCC
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-16-5p(1), mmu-miR-199a-5p(1), mmu-miR-433-5p(1), mmu-miR-382-3p(1), mmu-miR-411-3p(1)
siRNAs for circular RNA silencing
Junction sequence
ACGAGTCCTGCAGGATCTCCAGCACC
siRNA sets
NA
Protein-coding potential of circular RNAs
CPAT analysis
CPAT ORF ID
CPAT Fickett
CPAT Hexamer
Coding probabilty
ORF length
CIRCCOPB1_636_ORF_1
1.0319
0.068525666
0.995838262
1185
ORF sequence:
ATGCCTGCTATCCGTGCGTGCTTGGAACATCGTCACAGCTATGTTAGGAGAAATGCTGTTTTGGCCATCTATACCATCTACAGAAATTTTGAACATCTTATACCTGATGCTCCTGAACTGATACATGATTTTCTTGTGAATGAGAAGGATGCAAGCTGCAAAAGAAATGCATTTATGATGCTAATTCACGCAGATCAGGATCGAGCTTTGGATTATTTAAGTACATGTATTGATCAAGTTCAGACATTTGGAGACATTCTACAGTTGGTTATTGTTGAACTAATTTATAAGGTCTGTCATGCTAATCCATCAGAAAGGGCCCGCTTCATTCGCTGTATCTATAACTTACTGCAGTCATCTAGTCCTGCTGTAAAATATGAGGCTGCTGGGACACTGGTAACACTGTCAAGTGCACCAACTGCAATAAAGGCTGCTGCTCAGTGTTACATTGATTTAATTATTAAGGAGAGTGATAACAATGTAAAGCTCATCGTCCTGGACCGCTTGGTGGAATTAAAAGAGCATCCTGCTCATGAACGAGTCCTGCAGGATCTCCAGCACCCCAATGAGTTTATTCGTGGATCTACTCTTCGTTTCCTTTGCAAATTGAAGGAAGCAGAATTGCTGGAACCTTTAATGCCTGCTATCCGTGCGTGCTTGGAACATCGTCACAGCTATGTTAGGAGAAATGCTGTTTTGGCCATCTATACCATCTACAGAAATTTTGAACATCTTATACCTGATGCTCCTGAACTGATACATGATTTTCTTGTGAATGAGAAGGATGCAAGCTGCAAAAGAAATGCATTTATGATGCTAATTCACGCAGATCAGGATCGAGCTTTGGATTATTTAAGTACATGTATTGATCAAGTTCAGACATTTGGAGACATTCTACAGTTGGTTATTGTTGAACTAATTTATAAGGTCTGTCATGCTAATCCATCAGAAAGGGCCCGCTTCATTCGCTGTATCTATAACTTACTGCAGTCATCTAGTCCTGCTGTAAAATATGAGGCTGCTGGGACACTGGTAACACTGTCAAGTGCACCAACTGCAATAAAGGCTGCTGCTCAGTGTTACATTGATTTAATTATTAAGGAGAGTGATAACAATGTAAAGCTCATCGTCCTGGACCGCTTGGTGGAATTAAAAGAGCATCCTGCTCATGAACGAGTCCTGCAG
Peptide sequence:
MPAIRACLEHRHSYVRRNAVLAIYTIYRNFEHLIPDAPELIHDFLVNEKDASCKRNAFMMLIHADQDRALDYLSTCIDQVQTFGDILQLVIVELIYKVCHANPSERARFIRCIYNLLQSSSPAVKYEAAGTLVTLSSAPTAIKAAAQCYIDLIIKESDNNVKLIVLDRLVELKEHPAHERVLQDLQHPNEFIRGSTLRFLCKLKEAELLEPLMPAIRACLEHRHSYVRRNAVLAIYTIYRNFEHLIPDAPELIHDFLVNEKDASCKRNAFMMLIHADQDRALDYLSTCIDQVQTFGDILQLVIVELIYKVCHANPSERARFIRCIYNLLQSSSPAVKYEAAGTLVTLSSAPTAIKAAAQCYIDLIIKESDNNVKLIVLDRLVELKEHPAHERVLQ
IRESfinder result
IRESfinder score
0.723426542
IRES/non IRES
IRES
riboCIRC information
riboCIRC ID
NA
NA
Evidence
Peptide sequence:
NA
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