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mmu_circCcar1_436
Basic information of circular RNA
PanCircBase ID:
mmu_circCcar1_436
mm39_Chr. Position ID:
chr10|62616219|62621373|-
Gene name:
Ccar1
Transcript:
ENSMUST00000020268.7
CircRNA type:
Exonic circular (circ)RNA
Exon/Intron count:
4
Exon/intron indexes:
6,5,4,3
Exon/intron offsets:
0,2793,3442,4990
Genomic length:
5154
Exon/intron sizes in nt:
194,33,45,164
Flanking exon/introns:
chr10:62612742-62616219|chr10:62621373-62626699
Splice length:
436
Other database IDs:
circBase: mmu_circ_0002340, CIRCpedia: MMU_CIRCpedia_25392, circAtlas: mmu-Ccar1_0002
circBase: hsa_circ_0018542, circAtlas: hsa-CCAR1_0004, CIRCpedia: HSA_CIRCpedia_2110
Human Ortholog IDs:
Mature spliced Sequence:
CTGCACTAGGTGTTCAGCAGCCATCACTTCTGGGAGCATCTCCTACCATTTATACCCAGCAGACTGCATTGGCGGCGGCAGGCCTTACCACACAAACGCCAGCAAACTATCAGTTAACACAAACTGCGGCACTGCAGCAACAAGCTGCAGCTGTATTACAGCAGCAATATTCACAACCTCAGCAGGCCTTGTATAGTGTGCAGCAGCAGTTGCAACAACCTCAGCAGACCATTTTAACACAGCCAGCTGTTGCATTGCCCACAAGCCTTAGCCTGTCGACTCCTCAGCCTGCAGCACAGATTACTGTATCATATCCAACACCAAGGTCCAGTCAACAGCAAACTCAACCTCAGAAGCAGCGTGTTTTCACAGGAGTGGTTACAAAGCTACATGATACATTTGGATTTGTGGATGAAGATGTATTCTTTCAGCTTGG
Divergent primers for circular RNA PCR
Primer Set-1
Forward primer
Tm
Reverse primer
Tm
Product size
ACCTCAGAAGCAGCGTGTTT
60.18
CCAATGCAGTCTGCTGGGTA
60.04
162
Primer Set-2
Forward primer
Tm
Reverse primer
Tm
Product size
AACCTCAGAAGCAGCGTGTT
60.18
CCAATGCAGTCTGCTGGGTA
60.04
163
PCR template sequence:
AGCAAACTCAACCTCAGAAGCAGCGTGTTTTCACAGGAGTGGTTACAAAGCTACATGATACATTTGGATTTGTGGATGAAGATGTATTCTTTCAGCTTGGCTGCACTAGGTGTTCAGCAGCCATCACTTCTGGGAGCATCTCCTACCATTTATACCCAGCAGACTGCATTGGCGGCGGCAGGCCTTACCACACAAACGCC
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-137-3p(1), mmu-miR-34c-5p(1), mmu-miR-34a-5p(1), mmu-miR-101b-3p(1), mmu-miR-381-3p(1), mmu-miR-370-3p(1), mmu-miR-34b-5p(1)
siRNAs for circular RNA silencing
Junction sequence
TCTTTCAGCTTGGCTGCACTAGGTGT
siRNA sets
NA
Protein-coding potential of circular RNAs
CPAT analysis
CPAT ORF ID
CPAT Fickett
CPAT Hexamer
Coding probabilty
ORF length
CIRCCCAR1_436_ORF_1
1.0655
0.010059116
0.555502995
480
ORF sequence:
ATGATACATTTGGATTTGTGGATGAAGATGTATTCTTTCAGCTTGGCTGCACTAGGTGTTCAGCAGCCATCACTTCTGGGAGCATCTCCTACCATTTATACCCAGCAGACTGCATTGGCGGCGGCAGGCCTTACCACACAAACGCCAGCAAACTATCAGTTAACACAAACTGCGGCACTGCAGCAACAAGCTGCAGCTGTATTACAGCAGCAATATTCACAACCTCAGCAGGCCTTGTATAGTGTGCAGCAGCAGTTGCAACAACCTCAGCAGACCATTTTAACACAGCCAGCTGTTGCATTGCCCACAAGCCTTAGCCTGTCGACTCCTCAGCCTGCAGCACAGATTACTGTATCATATCCAACACCAAGGTCCAGTCAACAGCAAACTCAACCTCAGAAGCAGCGTGTTTTCACAGGAGTGGTTACAAAGCTACATGATACATTTGGATTTGTGGATGAAGATGTATTCTTTCAGCTT
Peptide sequence:
MIHLDLWMKMYSFSLAALGVQQPSLLGASPTIYTQQTALAAAGLTTQTPANYQLTQTAALQQQAAAVLQQQYSQPQQALYSVQQQLQQPQQTILTQPAVALPTSLSLSTPQPAAQITVSYPTPRSSQQQTQPQKQRVFTGVVTKLHDTFGFVDEDVFFQL
IRESfinder result
IRESfinder score
0.653197759
IRES/non IRES
IRES
riboCIRC information
riboCIRC ID
NA
NA
Evidence
Peptide sequence:
NA
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