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mmu_circKdm2a_286
Basic information of circular RNA
PanCircBase ID:
mmu_circKdm2a_286
mm39_Chr. Position ID:
chr19|4402295|4406954|-
Gene name:
Kdm2a
Transcript:
ENSMUST00000047898.14
CircRNA type:
Exonic circular (circ)RNA
Exon/Intron count:
2
Exon/intron indexes:
7,6
Exon/intron offsets:
0,4480
Genomic length:
4659
Exon/intron sizes in nt:
1,07,179
Flanking exon/introns:
chr19:4401858-4402295|chr19:4406954-4411565
Splice length:
286
Other database IDs:
circAtlas: hsa-SCAF8_0001, CIRCpedia: HSA_CIRCpedia_5199
Human Ortholog IDs:
Mature spliced Sequence:
GGAGTCGTCGGATGGTGGATGTCATGGATGTGAACACACAGAAGGGGATTGAAATGACCATGGCACAATGGACACGATACTATGAGACTCCAGAGGAAGAGCGAGAAAAACTCTATAATGTTATCAGCCTAGAGTTTAGCCACACCAGGCTTGAGAATATGGTGCAGCGGCCTTCCACGGTGGATTTCATTGACTGGGTAGATAACATGTGGCCAAGGCACTTGAAAGAAAGTCAGACAGAATCAACAAATGCCATCTTAGAGATGCAGTACCCTAAAGTGCAAAA
Divergent primers for circular RNA PCR
Primer Set-1
Forward primer
Tm
Reverse primer
Tm
Product size
AGATAACATGTGGCCAAGGCA
59.99
TGTCCATTGTGCCATGGTCA
59.89
161
Primer Set-2
Forward primer
Tm
Reverse primer
Tm
Product size
AGATAACATGTGGCCAAGGCA
59.99
GTGTCCATTGTGCCATGGTC
59.47
162
PCR template sequence:
TCATTGACTGGGTAGATAACATGTGGCCAAGGCACTTGAAAGAAAGTCAGACAGAATCAACAAATGCCATCTTAGAGATGCAGTACCCTAAAGTGCAAAAGGAGTCGTCGGATGGTGGATGTCATGGATGTGAACACACAGAAGGGGATTGAAATGACCATGGCACAATGGACACGATACTATGAGACTCCAGAGGAAGA
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
CTAAAGTGCAAAAGGAGTCGTCGGAT
siRNA sets
ATCCGACGACTCCTTTTGC, TCCGACGACTCCTTTTGCA
Protein-coding potential of circular RNAs
CPAT analysis
CPAT ORF ID
CPAT Fickett
CPAT Hexamer
Coding probabilty
ORF length
CIRCKDM2A_286_ORF_1
0.9194
0.250872501
0.459762777
327
ORF sequence:
ATGGTGGATGTCATGGATGTGAACACACAGAAGGGGATTGAAATGACCATGGCACAATGGACACGATACTATGAGACTCCAGAGGAAGAGCGAGAAAAACTCTATAATGTTATCAGCCTAGAGTTTAGCCACACCAGGCTTGAGAATATGGTGCAGCGGCCTTCCACGGTGGATTTCATTGACTGGGTAGATAACATGTGGCCAAGGCACTTGAAAGAAAGTCAGACAGAATCAACAAATGCCATCTTAGAGATGCAGTACCCTAAAGTGCAAAAGGAGTCGTCGGATGGTGGATGTCATGGATGTGAACACACAGAAGGGGATTGA
Peptide sequence:
MVDVMDVNTQKGIEMTMAQWTRYYETPEEEREKLYNVISLEFSHTRLENMVQRPSTVDFIDWVDNMWPRHLKESQTESTNAILEMQYPKVQKESSDGGCHGCEHTEGD
IRESfinder result
IRESfinder score
0.256518755
IRES/non IRES
non-IRES
riboCIRC information
riboCIRC ID
NA
NA
Evidence
Peptide sequence:
NA
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