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mmu_circRfx6_449
Basic information of circular RNA
PanCircBase ID:
mmu_circRfx6_449
mm39_Chr. Position ID:
chr10|51554380|51571123|+
Gene name:
Rfx6
Transcript:
ENSMUST00000217662.2
CircRNA type:
Exonic circular (circ)RNA
Exon/Intron count:
5
Exon/intron indexes:
2,3,4,5,6
Exon/intron offsets:
0,3525,5295,15411,16715
Genomic length:
16743
Exon/intron sizes in nt:
157,124,62,78,28
Flanking exon/introns:
chr10:51554125-51554380|chr10:51571123-51584670
Splice length:
449
Other database IDs:
Human Ortholog IDs:
Mature spliced Sequence:
AAATGCAGTTAAACAACGGCAACTTTTCCTCGGAAGAAGAGGATGCGGACACCCAGGAGAGCAAGACCAAAGCAGCCGACCCACAGCTCTCTCAGAAGAAGAGCATCACGCAGATGATGAAGGATAAGAAGAAGCAGACTCAGCTCACCCTGCAGTGGCTTGAAGACAATTACATAGTGTGTGAAGGAGTTTGCCTCCCACGGTGCATTCTTTATGCTCACTACCTAGATTTCTGCAGGAAAGAGAAACTGGAGCCAGCTTGTGCAGCCACCTTTGGAAAGACAATTCGCCAAAAATTTCCCCTCCTAACAACTCGAAGACTTGGAACAAGAGGACATTCAAAGTACCATTACTATGGGATTGGCATCAAAGAAAGCAGTGCATATTACCACTCTGTTTATTCTGGAAAGGGCTTGACAAGGTTTTCGGGGAGCAAACTGAAGAATGAG
Divergent primers for circular RNA PCR
Primer Set-1
Forward primer
Tm
Reverse primer
Tm
Product size
GGCATCAAAGAAAGCAGTGCA
60
GTCTTGCTCTCCTGGGTGTC
60.04
154
Primer Set-2
Forward primer
Tm
Reverse primer
Tm
Product size
TGGCATCAAAGAAAGCAGTGC
60
GTCTTGCTCTCCTGGGTGTC
60.04
155
PCR template sequence:
TTACTATGGGATTGGCATCAAAGAAAGCAGTGCATATTACCACTCTGTTTATTCTGGAAAGGGCTTGACAAGGTTTTCGGGGAGCAAACTGAAGAATGAGAAATGCAGTTAAACAACGGCAACTTTTCCTCGGAAGAAGAGGATGCGGACACCCAGGAGAGCAAGACCAAAGCAGCCGACCCACAGCTCTCTCAGAAGAA
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-149-5p(1), mmu-miR-501-3p(1), mmu-miR-705(1)
siRNAs for circular RNA silencing
Junction sequence
ACTGAAGAATGAGAAATGCAGTTAAA
siRNA sets
TTAACTGCATTTCTCATTC, TAACTGCATTTCTCATTCT, TTTAACTGCATTTCTCATT
Protein-coding potential of circular RNAs
CPAT analysis
CPAT ORF ID
CPAT Fickett
CPAT Hexamer
Coding probabilty
ORF length
CIRCRFX6_449_ORF_1
0.7031
0.185935424
0.528938842
459
ORF sequence:
ATGCAGTTAAACAACGGCAACTTTTCCTCGGAAGAAGAGGATGCGGACACCCAGGAGAGCAAGACCAAAGCAGCCGACCCACAGCTCTCTCAGAAGAAGAGCATCACGCAGATGATGAAGGATAAGAAGAAGCAGACTCAGCTCACCCTGCAGTGGCTTGAAGACAATTACATAGTGTGTGAAGGAGTTTGCCTCCCACGGTGCATTCTTTATGCTCACTACCTAGATTTCTGCAGGAAAGAGAAACTGGAGCCAGCTTGTGCAGCCACCTTTGGAAAGACAATTCGCCAAAAATTTCCCCTCCTAACAACTCGAAGACTTGGAACAAGAGGACATTCAAAGTACCATTACTATGGGATTGGCATCAAAGAAAGCAGTGCATATTACCACTCTGTTTATTCTGGAAAGGGCTTGACAAGGTTTTCGGGGAGCAAACTGAAGAATGAGAAATGCAGTTAA
Peptide sequence:
MQLNNGNFSSEEEDADTQESKTKAADPQLSQKKSITQMMKDKKKQTQLTLQWLEDNYIVCEGVCLPRCILYAHYLDFCRKEKLEPACAATFGKTIRQKFPLLTTRRLGTRGHSKYHYYGIGIKESSAYYHSVYSGKGLTRFSGSKLKNEKCS
IRESfinder result
IRESfinder score
0.59826938
IRES/non IRES
IRES
riboCIRC information
riboCIRC ID
NA
NA
Evidence
Peptide sequence:
NA
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