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mmu_ciRfx3_500
Basic information of circular RNA
PanCircBase ID:
mmu_ciRfx3_500
mm39_Chr. Position ID:
chr19|27987568|27988068|-
Gene name:
Rfx3
Transcript:
ENSMUST00000174420.2
CircRNA type:
Circular intronic (ci)RNA
Exon/Intron count:
1
Exon/intron indexes:
1
Exon/intron offsets:
0
Genomic length:
500
Exon/intron sizes in nt:
500
Flanking exon/introns:
chr19:27878303-27988068
Splice length:
500
Other database IDs:
Human Ortholog IDs:
Mature spliced Sequence:
GTCCGCGGGCGCCCAGGAGGAGGGGCAGGTGGAGAGAAGGGGCTCGCTTTCTCCCTCTCTCTTTCTTTAATTCGCTGCTTTGCAAAGCTGCCTGGTGGCTGCTGCTTTCCAAATCGAAATAGACAGCAGTGAGCAGGGGGGGTCCCCAAAAGGTGCTGCGCTGTGGTGGTTGTTGTTCACTTGCGGGGCCTTGTTGGGGGTTTTGTTATTTTTATCCTGGTACCTCGGTGAACTTTTCCCGAAGCCCGCTCCCTTCGTTTCGGCCCCTCTGTGCCTGCTGCTGAACGGACTGCACTTATTTGACCATCACTGGCCTCACGGGATTCTTTTTTTTTTTTTTTCTTTTAAAACTGTATTTTTCTTTGTGCTGCAAACAGTCTTAATATCCATTCAGCAGTCTTCTCCCCCCTTCCCCCCATTTGCACACACATTGAAACTAGGGGGCCTCTGCTGCTCTTGAGAGATTTTTTTTTTAAGTCTGTTTCTCTGTTTCTCTTCTC
Divergent primers for circular RNA PCR
Primer Set-1
Forward primer
Tm
Reverse primer
Tm
Product size
CCCCCATTTGCACACACATT
59.31
GAGAGAGGGAGAAAGCGAGC
59.9
149
Primer Set-2
Forward primer
Tm
Reverse primer
Tm
Product size
GCCTCTGCTGCTCTTGAGAG
60.46
CACCAGGCAGCTTTGCAAAG
60.6
154
PCR template sequence:
TCTCCCCCCTTCCCCCCATTTGCACACACATTGAAACTAGGGGGCCTCTGCTGCTCTTGAGAGATTTTTTTTTTAAGTCTGTTTCTCTGTTTCTCTTCTCGTCCGCGGGCGCCCAGGAGGAGGGGCAGGTGGAGAGAAGGGGCTCGCTTTCTCCCTCTCTCTTTCTTTAATTCGCTGCTTTGCAAAGCTGCCTGGTGGCT
Note: Users can design additional primers for provided template sequence using Primer3 or NCBI primer-blast.
miRNAs associated with circular RNAs
No of miRNAs
10
Interacting miRNAs (#binding sites)
mmu-miR-15b-5p(2), mmu-miR-16-5p(1), mmu-miR-15a-5p(1), mmu-miR-93-5p(1), mmu-miR-214-3p(1), mmu-miR-503-5p(1), mmu-miR-499-5p(1), mmu-miR-466a-5p(1), mmu-miR-1187(1), mmu-miR-466p-5p(1)
siRNAs for circular RNA silencing
Junction sequence
TGTTTCTCTTCTCGTCCGCGGGCGCC
siRNA sets
NA
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
0.944229698
IRES/non IRES
IRES
riboCIRC information
riboCIRC ID
NA
NA
Evidence
Peptide sequence:
NA
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