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mmu_circCarf_400
Basic information of circular RNA
PanCircBase ID:
mmu_circCarf_400
mm39_Chr. Position ID:
chr1|60141785|60147359|+
Gene name:
Carf
Transcript:
ENSMUST00000130075.8
CircRNA type:
Exonic circular (circ)RNA
Exon/Intron count:
3
Exon/intron indexes:
2,3,4
Exon/intron offsets:
0,2684,5456
Genomic length:
5574
Exon/intron sizes in nt:
15,81,24,118
Flanking exon/introns:
chr1:60137466-60141785|chr1:60147359-60148485
Splice length:
400
Other database IDs:
circAtlas: mmu-Carf_0042
Human Ortholog IDs:
Mature spliced Sequence:
AGAACATGCTACCGTGAAGGCACAGTCACAGCTTTCACATAAGCACGCGGCTGGCACTGTTATAATTTAGTGCCCCAAAGGAAGACCCTCAATGAACGGGCATTTCTGAGGCAGAGTACATAGGCATCTGGACTTGAGACTTGAGCCACTGCCTGAAGGTATGGTGAGATCAACAGAGGAAGAGACAATTGACATTGGGAAACCAGCCCACTATTCACAGTTCTCAAAAGGAGTGGCCATGCTGTACCACAAAGTGCCAACAATATAACACCAAGGTCAGTGCCATTAACTAATCAGAGAAAATGGAACTGAATGTGAAGCCAGCATGGAGCAGCGTCATTCCTTAGCGGGCAACTGTGACGATGGTGAGAAGTCAGAAAGAGAGGCTCAGGGATTCGAG
Divergent primers for circular RNA PCR
Primer Set-1
Forward primer
Tm
Reverse primer
Tm
Product size
ATGGAGCAGCGTCATTCCTT
59.75
GGTCTTCCTTTGGGGCACTA
59.3
162
Primer Set-2
Forward primer
Tm
Reverse primer
Tm
Product size
CATGGAGCAGCGTCATTCCT
60.46
GGTCTTCCTTTGGGGCACTA
59.3
163
PCR template sequence:
AAATGGAACTGAATGTGAAGCCAGCATGGAGCAGCGTCATTCCTTAGCGGGCAACTGTGACGATGGTGAGAAGTCAGAAAGAGAGGCTCAGGGATTCGAGAGAACATGCTACCGTGAAGGCACAGTCACAGCTTTCACATAAGCACGCGGCTGGCACTGTTATAATTTAGTGCCCCAAAGGAAGACCCTCAATGAACGGG
Note: Users can design additional primers for provided template sequence using Primer3 or NCBI primer-blast.
miRNAs associated with circular RNAs
No of miRNAs
12
Interacting miRNAs (#binding sites)
mmu-miR-29b-1-5p(2), mmu-miR-34a-5p(1), mmu-miR-320-3p(1), mmu-miR-125b-5p(1), mmu-miR-181b-5p(1), mmu-miR-136-5p(1), mmu-miR-351-5p(1), mmu-miR-125a-5p(1), mmu-miR-183-5p(1), mmu-miR-29b-2-5p(1), mmu-miR-670-5p(1), mmu-miR-181d-5p(1)
siRNAs for circular RNA silencing
Junction sequence
TCAGGGATTCGAGAGAACATGCTACC
siRNA sets
CATGTTCTCTCGAATCCCT, AGCATGTTCTCTCGAATCC, ATGTTCTCTCGAATCCCTG
Protein-coding potential of circular RNAs
CPAT analysis
CPAT ORF ID
CPAT Fickett
CPAT Hexamer
Coding probabilty
ORF length
CIRCCARF_400_ORF_1
0.991
0.197724199
0.146016189
117
ORF sequence:
ATGGAGCAGCGTCATTCCTTAGCGGGCAACTGTGACGATGGTGAGAAGTCAGAAAGAGAGGCTCAGGGATTCGAGAGAACATGCTACCGTGAAGGCACAGTCACAGCTTTCACATAA
Peptide sequence:
MEQRHSLAGNCDDGEKSEREAQGFERTCYREGTVTAFT
IRESfinder result
IRESfinder score
0.600841781
IRES/non IRES
IRES
riboCIRC information
riboCIRC ID
NA
NA
Evidence
Peptide sequence:
NA
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