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mmu_circKdm2a_240
Basic information of circular RNA
PanCircBase ID:
mmu_circKdm2a_240
mm39_Chr. Position ID:
chr19|4412803|4444920|-
Gene name:
Kdm2a
Transcript:
ENSMUST00000047898.14
CircRNA type:
Exonic circular (circ)RNA
Exon/Intron count:
2
Exon/intron indexes:
3,2
Exon/intron offsets:
0,32016
Genomic length:
32117
Exon/intron sizes in nt:
1,39,101
Flanking exon/introns:
chr19:4412083-4412803|chr19:4444920-4447961
Splice length:
240
Other database IDs:
circAtlas: mmu-Kdm2a_0030
Human Ortholog IDs:
Mature spliced Sequence:
GAAGAGGAAGGCATCCCTGGAGTGGTTTCTTTACTGTACTTCCATCAGAAGAGTGAGAGATGGAACCTGAAGAAGAAAGGATTCGGTACAGCCAGAGATTGCGTGGTACCATGCGTCGTCGCTATGAAGATGATGGCATTTCAGATGATGAAATTGAAGGGAAAAGAACTTTTGACTTGGAAGAGAAGCTCCAAACCAACAAATATAATGCCAATTTTGTTACTTTTATGGAGGGAAAAG
Divergent primers for circular RNA PCR
Primer Set-1
Forward primer
Tm
Reverse primer
Tm
Product size
TGGAAGAGAAGCTCCAAACCA
59.23
TCTCTGGCTGTACCGAATCC
58.89
161
Primer Set-2
Forward primer
Tm
Reverse primer
Tm
Product size
TGGAAGAGAAGCTCCAAACCA
59.23
CTCTGGCTGTACCGAATCCT
58.88
160
PCR template sequence:
TCAGATGATGAAATTGAAGGGAAAAGAACTTTTGACTTGGAAGAGAAGCTCCAAACCAACAAATATAATGCCAATTTTGTTACTTTTATGGAGGGAAAAGGAAGAGGAAGGCATCCCTGGAGTGGTTTCTTTACTGTACTTCCATCAGAAGAGTGAGAGATGGAACCTGAAGAAGAAAGGATTCGGTACAGCCAGAGATT
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
ATGGAGGGAAAAGGAAGAGGAAGGCA
siRNA sets
TTCCTCTTCCTTTTCCCTC, CTTCCTCTTCCTTTTCCCT, TCCTCTTCCTTTTCCCTCC
Protein-coding potential of circular RNAs
CPAT analysis
CPAT ORF ID
CPAT Fickett
CPAT Hexamer
Coding probabilty
ORF length
CIRCKDM2A_240_ORF_1
1.0805
-0.03629451
0.306371035
357
ORF sequence:
ATGAAGATGATGGCATTTCAGATGATGAAATTGAAGGGAAAAGAACTTTTGACTTGGAAGAGAAGCTCCAAACCAACAAATATAATGCCAATTTTGTTACTTTTATGGAGGGAAAAGGAAGAGGAAGGCATCCCTGGAGTGGTTTCTTTACTGTACTTCCATCAGAAGAGTGAGAGATGGAACCTGAAGAAGAAAGGATTCGGTACAGCCAGAGATTGCGTGGTACCATGCGTCGTCGCTATGAAGATGATGGCATTTCAGATGATGAAATTGAAGGGAAAAGAACTTTTGACTTGGAAGAGAAGCTCCAAACCAACAAATATAATGCCAATTTTGTTACTTTTATGGAGGGAAAAG
Peptide sequence:
MKMMAFQMMKLKGKELLTWKRSSKPTNIMPILLLLWREKEEEGIPGVVSLLYFHQKSERWNLKKKGFGTARDCVVPCVVAMKMMAFQMMKLKGKELLTWKRSSKPTNIMPILLLLWREK
IRESfinder result
IRESfinder score
0.411240791
IRES/non IRES
non-IRES
riboCIRC information
riboCIRC ID
NA
NA
Evidence
Peptide sequence:
NA
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