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mmu_ciNedd4_237
Basic information of circular RNA
PanCircBase ID:
mmu_ciNedd4_237
mm39_Chr. Position ID:
chr9|72638255|72638492|+
Gene name:
Nedd4
Transcript:
ENSMUST00000034740.15
CircRNA type:
Circular intronic (ci)RNA
Exon/Intron count:
1
Exon/intron indexes:
15
Exon/intron offsets:
0
Genomic length:
237
Exon/intron sizes in nt:
237
Flanking exon/introns:
chr9:72638255-72638503
Splice length:
237
Other database IDs:
Human Ortholog IDs:
Mature spliced Sequence:
GTAAGTTCTCCTGCTGAGCTCACTTCACTATTTCAGACATTTTGTACCTTGGGATGCTGGAGTTACTTAACAACTATAACTAACATTGTTAATAAGTTATTGATGCCTTTCGTTTTAAGTGTTATGTACAAATTAAGCATATATGCAATATGAGATCTTCTATTTCTGTTTCTTTTTTTTTTTTTTTTAAATAACCTGTACATCTAAGACCTGGTACTAAAATAATTGCAATGAATG
Divergent primers for circular RNA PCR
Primer Set-1
Forward primer
Tm
Reverse primer
Tm
Product size
TGCAATATGAGATCTTCTATTTCTGT
56.57
CTCCAGCATCCCAAGGTACA
59.09
156
Primer Set-2
Forward primer
Tm
Reverse primer
Tm
Product size
TGCAATATGAGATCTTCTATTTCTGT
56.57
ACTCCAGCATCCCAAGGTAC
59.09
157
PCR template sequence:
CATATATGCAATATGAGATCTTCTATTTCTGTTTCTTTTTTTTTTTTTTTTAAATAACCTGTACATCTAAGACCTGGTACTAAAATAATTGCAATGAATGGTAAGTTCTCCTGCTGAGCTCACTTCACTATTTCAGACATTTTGTACCTTGGGATGCTGGAGTTACTTAACAACTATAACTAACATTGTTAATAAGTTAT
Note: Users can design additional primers for provided template sequence using Primer3 or NCBI primer-blast.
miRNAs associated with circular RNAs
No of miRNAs
NA
Interacting miRNAs (#binding sites)
NA
siRNAs for circular RNA silencing
Junction sequence
ATTGCAATGAATGGTAAGTTCTCCTG
siRNA sets
AGAACTTACCATTCATTGC, GAACTTACCATTCATTGCA, AACTTACCATTCATTGCAA
Protein-coding potential of circular RNAs
CPAT analysis
CPAT ORF ID
CPAT Fickett
CPAT Hexamer
Coding probabilty
ORF length
CINEDD4_237_ORF_1
0.6268
-0.446792224
0.008247467
156
ORF sequence:
ATGGTAAGTTCTCCTGCTGAGCTCACTTCACTATTTCAGACATTTTGTACCTTGGGATGCTGGAGTTACTTAACAACTATAACTAACATTGTTAATAAGTTATTGATGCCTTTCGTTTTAAGTGTTATGTACAAATTAAGCATATATGCAATATGA
Peptide sequence:
MVSSPAELTSLFQTFCTLGCWSYLTTITNIVNKLLMPFVLSVMYKLSIYAI
IRESfinder result
IRESfinder score
0.955798373
IRES/non IRES
IRES
riboCIRC information
riboCIRC ID
NA
NA
Evidence
Peptide sequence:
NA
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