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mmu_circCdc27_448
Basic information of circular RNA
PanCircBase ID:
mmu_circCdc27_448
mm39_Chr. Position ID:
chr11|104420166|104427496|-
Gene name:
Cdc27
Transcript:
ENSMUST00000093923.9
CircRNA type:
Exonic circular (circ)RNA
Exon/Intron count:
4
Exon/intron indexes:
5,4,3,2
Exon/intron offsets:
0,2389,5397,7254
Genomic length:
7330
Exon/intron sizes in nt:
98,126,148,76
Flanking exon/introns:
chr11:104419558-104420166|chr11:104427496-104441188
Splice length:
448
Other database IDs:
CIRCpedia: MMU_CIRCpedia_1277, circAtlas: mmu-Cdc27_0050
Human Ortholog IDs:
Mature spliced Sequence:
GCTGCTATATGGCAAGCGCTAAACCACTATGCTTACCGAGATGCAGTTTTCCTCGCAGAACGACTATATGCAGAAGTACATTCAGAAGAAGCCTTGTTTTTACTGGCAACCTGTTACTACCGCTCAGGAAAGGCTTATAAAGCATATAGACTCTTGAAAGGACACAGTTGTACCACCCCACAGTGTAAATACCTGCTTGCAAAATGTTGTGTTGACCTCAGCAAGCTTGCAGAAGGGGAACAGATCTTATCTGGTGGAGTGTTTAATAAGCAGAAAAGCCATGACGACCTTGTCACTGAGTTTGGAGATTCAGCTTGCTTCACTCTTTCCTTGTTGGGACATGTGTATTGCAAGACAGATCGGCTTGCCAAAGGGTCAGAATGTTACCAAAAGAGCCTTAGTTTAAATCCTTTCCTCTGGTCTCCCTTTGAATCGTTATGTGAAATAG
Divergent primers for circular RNA PCR
Primer Set-1
Forward primer
Tm
Reverse primer
Tm
Product size
AGACAGATCGGCTTGCCAAA
59.96
CGTTCTGCGAGGAAAACTGC
60.11
158
Primer Set-2
Forward primer
Tm
Reverse primer
Tm
Product size
AAGACAGATCGGCTTGCCAA
59.96
CGTTCTGCGAGGAAAACTGC
60.11
159
PCR template sequence:
TGCAAGACAGATCGGCTTGCCAAAGGGTCAGAATGTTACCAAAAGAGCCTTAGTTTAAATCCTTTCCTCTGGTCTCCCTTTGAATCGTTATGTGAAATAGGCTGCTATATGGCAAGCGCTAAACCACTATGCTTACCGAGATGCAGTTTTCCTCGCAGAACGACTATATGCAGAAGTACATTCAGAAGAAGCCTTGTTTT
Note: Users can design additional primers for provided template sequence using Primer3 or NCBI primer-blast.
miRNAs associated with circular RNAs
No of miRNAs
4
Interacting miRNAs (#binding sites)
mmu-miR-140-5p(1), mmu-miR-135a-5p(1), mmu-miR-431-5p(1), mmu-miR-3105-3p(1)
siRNAs for circular RNA silencing
Junction sequence
TTATGTGAAATAGGCTGCTATATGGC
siRNA sets
ATATAGCAGCCTATTTCAC, TATAGCAGCCTATTTCACA, ATAGCAGCCTATTTCACAT
Protein-coding potential of circular RNAs
CPAT analysis
CPAT ORF ID
CPAT Fickett
CPAT Hexamer
Coding probabilty
ORF length
NA
NA
NA
NA
NA
ORF sequence:
NA
Peptide sequence:
NA
IRESfinder result
IRESfinder score
0.668069647
IRES/non IRES
IRES
riboCIRC information
riboCIRC ID
NA
NA
Evidence
Peptide sequence:
NA
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