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mmu_circKdm2a_652
Basic information of circular RNA
PanCircBase ID:
mmu_circKdm2a_652
mm39_Chr. Position ID:
chr19|4402295|4444920|-
Gene name:
Kdm2a
Transcript:
ENSMUST00000047898.14
CircRNA type:
Exonic circular (circ)RNA
Exon/Intron count:
6
Exon/intron indexes:
7,6,5,4,3,2
Exon/intron offsets:
0,4480,9270,9709,10508,42524
Genomic length:
42625
Exon/intron sizes in nt:
1,07,17,94,77,91,39,100
Flanking exon/introns:
chr19:4401858-4402295|chr19:4444920-4447961
Splice length:
652
Other database IDs:
circAtlas: mmu-Kdm2a_0031
Human Ortholog IDs:
Mature spliced Sequence:
GAAGAGGAAGGCATCCCTGGAGTGGTTTCTTTACTGTACTTCCATCAGAAGAGTGAGAGATGGAACCTGAAGAAGAAAGGATTCGGTACAGCCAGAGATTGCGTGGTACCATGCGTCGTCGCTATGAAGATGATGGCATTTCAGATGATGAAATTGAAGGGAAAAGAACTTTTGACTTGGAAGAGAAGCTCCAAACCAACAAATATAATGCCAATTTTGTTACTTTTATGGAGGGAAAAGATTTTAATGTAGAGTATATCCAGCGGGGTGGCTTGAGAGACCCTCTCATTTTCAAGAATTCTGATGGACTTGGAATAAAGATGCCGGATCCAGACTTCACAGTGAATGATGTCAAAATGTGTGTGGGGAGTCGTCGGATGGTGGATGTCATGGATGTGAACACACAGAAGGGGATTGAAATGACCATGGCACAATGGACACGATACTATGAGACTCCAGAGGAAGAGCGAGAAAAACTCTATAATGTTATCAGCCTAGAGTTTAGCCACACCAGGCTTGAGAATATGGTGCAGCGGCCTTCCACGGTGGATTTCATTGACTGGGTAGATAACATGTGGCCAAGGCACTTGAAAGAAAGTCAGACAGAATCAACAAATGCCATCTTAGAGATGCAGTACCCTAAAGTGCAAAA
Divergent primers for circular RNA PCR
Primer Set-1
Forward primer
Tm
Reverse primer
Tm
Product size
GATAACATGTGGCCAAGGCA
58.53
TGGCTGTACCGAATCCTTTCT
59.09
180
Primer Set-2
Forward primer
Tm
Reverse primer
Tm
Product size
AGATAACATGTGGCCAAGGCA
59.99
GGCTGTACCGAATCCTTTCT
57.31
180
PCR template sequence:
TCATTGACTGGGTAGATAACATGTGGCCAAGGCACTTGAAAGAAAGTCAGACAGAATCAACAAATGCCATCTTAGAGATGCAGTACCCTAAAGTGCAAAAGAAGAGGAAGGCATCCCTGGAGTGGTTTCTTTACTGTACTTCCATCAGAAGAGTGAGAGATGGAACCTGAAGAAGAAAGGATTCGGTACAGCCAGAGATT
Note: Users can design additional primers for provided template sequence using Primer3 or NCBI primer-blast.
miRNAs associated with circular RNAs
No of miRNAs
1
Interacting miRNAs (#binding sites)
mmu-miR-382-3p(1)
siRNAs for circular RNA silencing
Junction sequence
CTAAAGTGCAAAAGAAGAGGAAGGCA
siRNA sets
CTTCCTCTTCTTTTGCACT, TTCCTCTTCTTTTGCACTT, TGCCTTCCTCTTCTTTTGC
Protein-coding potential of circular RNAs
CPAT analysis
CPAT ORF ID
CPAT Fickett
CPAT Hexamer
Coding probabilty
ORF length
CIRCKDM2A_652_ORF_1
0.9006
0.244153018
0.898789906
663
ORF sequence:
ATGGAACCTGAAGAAGAAAGGATTCGGTACAGCCAGAGATTGCGTGGTACCATGCGTCGTCGCTATGAAGATGATGGCATTTCAGATGATGAAATTGAAGGGAAAAGAACTTTTGACTTGGAAGAGAAGCTCCAAACCAACAAATATAATGCCAATTTTGTTACTTTTATGGAGGGAAAAGATTTTAATGTAGAGTATATCCAGCGGGGTGGCTTGAGAGACCCTCTCATTTTCAAGAATTCTGATGGACTTGGAATAAAGATGCCGGATCCAGACTTCACAGTGAATGATGTCAAAATGTGTGTGGGGAGTCGTCGGATGGTGGATGTCATGGATGTGAACACACAGAAGGGGATTGAAATGACCATGGCACAATGGACACGATACTATGAGACTCCAGAGGAAGAGCGAGAAAAACTCTATAATGTTATCAGCCTAGAGTTTAGCCACACCAGGCTTGAGAATATGGTGCAGCGGCCTTCCACGGTGGATTTCATTGACTGGGTAGATAACATGTGGCCAAGGCACTTGAAAGAAAGTCAGACAGAATCAACAAATGCCATCTTAGAGATGCAGTACCCTAAAGTGCAAAAGAAGAGGAAGGCATCCCTGGAGTGGTTTCTTTACTGTACTTCCATCAGAAGAGTGAGAGATGGAACCTGA
Peptide sequence:
MEPEEERIRYSQRLRGTMRRRYEDDGISDDEIEGKRTFDLEEKLQTNKYNANFVTFMEGKDFNVEYIQRGGLRDPLIFKNSDGLGIKMPDPDFTVNDVKMCVGSRRMVDVMDVNTQKGIEMTMAQWTRYYETPEEEREKLYNVISLEFSHTRLENMVQRPSTVDFIDWVDNMWPRHLKESQTESTNAILEMQYPKVQKKRKASLEWFLYCTSIRRVRDGT
IRESfinder result
IRESfinder score
0.364066767
IRES/non IRES
non-IRES
riboCIRC information
riboCIRC ID
NA
NA
Evidence
Peptide sequence:
NA
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