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mmu_circCdc123_747
Basic information of circular RNA
PanCircBase ID:
mmu_circCdc123_747
mm39_Chr. Position ID:
chr2|5800359|5828008|-
Gene name:
Cdc123
Transcript:
ENSMUST00000043864.9
CircRNA type:
Exonic circular (circ)RNA
Exon/Intron count:
8
Exon/intron indexes:
12,11,10,9,8,7,6,5
Exon/intron offsets:
0,2812,8398,9362,11882,15247,25727,27553
Genomic length:
27649
Exon/intron sizes in nt:
138,129,29,123,76,49,107,96
Flanking exon/introns:
chr2:5799691-5800359|chr2:5828008-5837891
Splice length:
747
Other database IDs:
circAtlas: mmu-Cdc123_0009
Human Ortholog IDs:
Mature spliced Sequence:
GCACCAGAGTTTCCTGAGTTCAACACTCAAGTCCAAGAAGCTATCAATTCGCTGGGGGGTAGTGTCTTCCCTAAGCTTAACTGGAGTGCCCCAAGGGATGCGTACTGGATAGCGATGAACAGTTCCCTGAAGTGTAAAACTCTCAGTGATATCTTCCTGCTTTTCAAGAGTTCTGATTTCATCACCCATGACTTCACACAGCCGTTTATTCATTGCACTGATGACTCTCCAGACCCTTGTATAGAGTACGAGCTTGTTCTCCGAAAATGGTGTGAATTAATTCCTGGGGCTGAATTCCGATGTTTTGTCAAAGAAAATAAGCTTATTGGTATTTCTCAGAGGGATTACACACAATACTATGATCATATTTCTAAGCAAAAAGAAGAAATTTGCAGATGCATTCAAGACTTTTTCAAGGAACACCTACAGTATAAATTCTTAGATGAAGACTTTGTGTTCGATATATACAGGGACAGTAGGGGGAAGGTGTGGCTCATTGACTTTAATCCATTTGGGGAGGTCACAGACTCACTGTTGTTTACTTGGGAAGAGCTAACATCTGAGAACAACCTACGTGGTGAGGTCACTGAAGGAGATGCTCAGGAGCAGGATTCTCCAGCCTTCCGTTGCACAAACAGTGAAGTCACAGTGCAGCCCAGCCCCTATCTGAGCTTCGGGCTGCCCAAGGACTTTGTAGACCTTTCCACCGGGGAGGATGCTCACAAGCTCATCGATTTCCTTAAGCTG
Divergent primers for circular RNA PCR
Primer Set-1
Forward primer
Tm
Reverse primer
Tm
Product size
CAGCCCCTATCTGAGCTTCG
59.97
CCCCCAGCGAATTGATAGCT
59.89
149
Primer Set-2
Forward primer
Tm
Reverse primer
Tm
Product size
GGCTGCCCAAGGACTTTGTA
60.25
GGGGCACTCCAGTTAAGCTT
59.96
163
PCR template sequence:
AGTGCAGCCCAGCCCCTATCTGAGCTTCGGGCTGCCCAAGGACTTTGTAGACCTTTCCACCGGGGAGGATGCTCACAAGCTCATCGATTTCCTTAAGCTGGCACCAGAGTTTCCTGAGTTCAACACTCAAGTCCAAGAAGCTATCAATTCGCTGGGGGGTAGTGTCTTCCCTAAGCTTAACTGGAGTGCCCCAAGGGATG
Note: Users can design additional primers for provided template sequence using Primer3 or NCBI primer-blast.
miRNAs associated with circular RNAs
No of miRNAs
12
Interacting miRNAs (#binding sites)
mmu-miR-30e-5p(1), mmu-miR-33-5p(1), mmu-miR-130a-3p(1), mmu-miR-152-3p(1), mmu-miR-324-5p(1), mmu-miR-381-3p(1), mmu-miR-433-5p(1), mmu-miR-127-5p(1), mmu-miR-130b-3p(1), mmu-miR-301b-3p(1), mmu-miR-721(1), mmu-miR-301a-3p(1)
siRNAs for circular RNA silencing
Junction sequence
TTTCCTTAAGCTGGCACCAGAGTTTC
siRNA sets
AAACTCTGGTGCCAGCTTA, TCTGGTGCCAGCTTAAGGA
Protein-coding potential of circular RNAs
CPAT analysis
CPAT ORF ID
CPAT Fickett
CPAT Hexamer
Coding probabilty
ORF length
CIRCCDC123_747_ORF_1
0.9674
0.168819439
0.999231076
1380
ORF sequence:
ATGAACAGTTCCCTGAAGTGTAAAACTCTCAGTGATATCTTCCTGCTTTTCAAGAGTTCTGATTTCATCACCCATGACTTCACACAGCCGTTTATTCATTGCACTGATGACTCTCCAGACCCTTGTATAGAGTACGAGCTTGTTCTCCGAAAATGGTGTGAATTAATTCCTGGGGCTGAATTCCGATGTTTTGTCAAAGAAAATAAGCTTATTGGTATTTCTCAGAGGGATTACACACAATACTATGATCATATTTCTAAGCAAAAAGAAGAAATTTGCAGATGCATTCAAGACTTTTTCAAGGAACACCTACAGTATAAATTCTTAGATGAAGACTTTGTGTTCGATATATACAGGGACAGTAGGGGGAAGGTGTGGCTCATTGACTTTAATCCATTTGGGGAGGTCACAGACTCACTGTTGTTTACTTGGGAAGAGCTAACATCTGAGAACAACCTACGTGGTGAGGTCACTGAAGGAGATGCTCAGGAGCAGGATTCTCCAGCCTTCCGTTGCACAAACAGTGAAGTCACAGTGCAGCCCAGCCCCTATCTGAGCTTCGGGCTGCCCAAGGACTTTGTAGACCTTTCCACCGGGGAGGATGCTCACAAGCTCATCGATTTCCTTAAGCTGGCACCAGAGTTTCCTGAGTTCAACACTCAAGTCCAAGAAGCTATCAATTCGCTGGGGGGTAGTGTCTTCCCTAAGCTTAACTGGAGTGCCCCAAGGGATGCGTACTGGATAGCGATGAACAGTTCCCTGAAGTGTAAAACTCTCAGTGATATCTTCCTGCTTTTCAAGAGTTCTGATTTCATCACCCATGACTTCACACAGCCGTTTATTCATTGCACTGATGACTCTCCAGACCCTTGTATAGAGTACGAGCTTGTTCTCCGAAAATGGTGTGAATTAATTCCTGGGGCTGAATTCCGATGTTTTGTCAAAGAAAATAAGCTTATTGGTATTTCTCAGAGGGATTACACACAATACTATGATCATATTTCTAAGCAAAAAGAAGAAATTTGCAGATGCATTCAAGACTTTTTCAAGGAACACCTACAGTATAAATTCTTAGATGAAGACTTTGTGTTCGATATATACAGGGACAGTAGGGGGAAGGTGTGGCTCATTGACTTTAATCCATTTGGGGAGGTCACAGACTCACTGTTGTTTACTTGGGAAGAGCTAACATCTGAGAACAACCTACGTGGTGAGGTCACTGAAGGAGATGCTCAGGAGCAGGATTCTCCAGCCTTCCGTTGCACAAACAGTGAAGTCACAGTGCAGCCCAGCCCCTATCTGAGCTTCGGGCTGCCCAAGGACTTTGTAGACCTTTCCACCGGGGAGGATGCTCACAAGCTCATCGATTTCCTTAAGCTG
Peptide sequence:
MNSSLKCKTLSDIFLLFKSSDFITHDFTQPFIHCTDDSPDPCIEYELVLRKWCELIPGAEFRCFVKENKLIGISQRDYTQYYDHISKQKEEICRCIQDFFKEHLQYKFLDEDFVFDIYRDSRGKVWLIDFNPFGEVTDSLLFTWEELTSENNLRGEVTEGDAQEQDSPAFRCTNSEVTVQPSPYLSFGLPKDFVDLSTGEDAHKLIDFLKLAPEFPEFNTQVQEAINSLGGSVFPKLNWSAPRDAYWIAMNSSLKCKTLSDIFLLFKSSDFITHDFTQPFIHCTDDSPDPCIEYELVLRKWCELIPGAEFRCFVKENKLIGISQRDYTQYYDHISKQKEEICRCIQDFFKEHLQYKFLDEDFVFDIYRDSRGKVWLIDFNPFGEVTDSLLFTWEELTSENNLRGEVTEGDAQEQDSPAFRCTNSEVTVQPSPYLSFGLPKDFVDLSTGEDAHKLIDFLKL
IRESfinder result
IRESfinder score
0.730894374
IRES/non IRES
IRES
riboCIRC information
riboCIRC ID
NA
NA
Evidence
Peptide sequence:
NA
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