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mmu_ciPcnx3_324
Basic information of circular RNA
PanCircBase ID:
mmu_ciPcnx3_324
mm39_Chr. Position ID:
chr19|5737700|5738024|-
Gene name:
Pcnx3
Transcript:
ENSMUST00000113615.9
CircRNA type:
Circular intronic (ci)RNA
Exon/Intron count:
1
Exon/intron indexes:
1
Exon/intron offsets:
0
Genomic length:
324
Exon/intron sizes in nt:
324
Flanking exon/introns:
chr19:5737666-5738024
Splice length:
324
Other database IDs:
Human Ortholog IDs:
Mature spliced Sequence:
GTGAGAGGCTGCCACCACCTGTAACTATGGCGAGAGGGAGTGTAGTCTGGAGGGATGGGCATCTTGAGTCCTGGGGCGTGGAGTGAAGCGAGTCACTGTAGAGTTCACTGTAGAGTTTACTTTGGTTTTATATAGAGGAAAGACCAAGTCTTTTCTGCATGGAGTGACCTTGAGCGCCTCATTTAATCTACCCGGTTAAACAGAGGGCTACCCCTAACAGGGCTCTTTGTACTGTTGCATGAAGGGGTGATGAAGTTTTGTAAACCGATGAATCCTAGTTCTTTACAGTGGTGGCAGGTACACCCTCAAGGGAGCAAGGGTTTT
Divergent primers for circular RNA PCR
Primer Set-1
Forward primer
Tm
Reverse primer
Tm
Product size
ACTGTTGCATGAAGGGGTGA
59.52
ACTACACTCCCTCTCGCCAT
60.03
140
Primer Set-2
Forward primer
Tm
Reverse primer
Tm
Product size
ACTGTTGCATGAAGGGGTGA
59.52
CTCAAGATGCCCATCCCTCC
59.89
162
PCR template sequence:
CTTTGTACTGTTGCATGAAGGGGTGATGAAGTTTTGTAAACCGATGAATCCTAGTTCTTTACAGTGGTGGCAGGTACACCCTCAAGGGAGCAAGGGTTTTGTGAGAGGCTGCCACCACCTGTAACTATGGCGAGAGGGAGTGTAGTCTGGAGGGATGGGCATCTTGAGTCCTGGGGCGTGGAGTGAAGCGAGTCACTGTA
Note: Users can design additional primers for provided template sequence using Primer3 or NCBI primer-blast.
miRNAs associated with circular RNAs
No of miRNAs
3
Interacting miRNAs (#binding sites)
mmu-miR-139-5p(2), mmu-miR-101a-3p(1), mmu-miR-205-5p(1)
siRNAs for circular RNA silencing
Junction sequence
GAGCAAGGGTTTTGTGAGAGGCTGCC
siRNA sets
CAGCCTCTCACAAAACCCT, TCTCACAAAACCCTTGCTC, CTCTCACAAAACCCTTGCT
Protein-coding potential of circular RNAs
CPAT analysis
CPAT ORF ID
CPAT Fickett
CPAT Hexamer
Coding probabilty
ORF length
CIPCNX3_324_ORF_1
0.8975
-0.233480326
0.021260675
99
ORF sequence:
ATGAAGTTTTGTAAACCGATGAATCCTAGTTCTTTACAGTGGTGGCAGGTACACCCTCAAGGGAGCAAGGGTTTTGTGAGAGGCTGCCACCACCTGTAA
Peptide sequence:
MKFCKPMNPSSLQWWQVHPQGSKGFVRGCHHL
IRESfinder result
IRESfinder score
0.683733707
IRES/non IRES
IRES
riboCIRC information
riboCIRC ID
NA
NA
Evidence
Peptide sequence:
NA
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