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mmu_circCdkl2_621
Basic information of circular RNA
PanCircBase ID:
mmu_circCdkl2_621
mm39_Chr. Position ID:
chr5|92164980|92168172|-
Gene name:
Cdkl2
Transcript:
ENSMUST00000069937.11
CircRNA type:
Exonic circular (circ)RNA
Exon/Intron count:
4
Exon/intron indexes:
12,11,10,9
Exon/intron offsets:
0,260,2257,2896
Genomic length:
3192
Exon/intron sizes in nt:
107,124,94,296
Flanking exon/introns:
chr5:92155993-92164980|chr5:92168172-92169961
Splice length:
621
Other database IDs:
Human Ortholog IDs:
Mature spliced Sequence:
GATACCAATGCTGACCCCAAAATTAAGGATTCAAAAGTATTTAAAGTAAAGGGGTCAAAAATTGATGTTGAGAAAATGGAAAAAGGAAGTAGAGCTTCAAATGCCAACTGTCTCCATGACAATGGGACAAACCACAAAGGCTTGGCTTCCACCAGCCTCAGAGATTGCAGCAATGTCAACATTGATCACTCAAGGAACCCAGGCACAGCGATTCCTCCCCTCACACACAATCTTTCTGCAGTTGCTCCTGGCATTAATGCTGGAATGGGGACTATTCCTGGCGTTCAGAATTACAGAGTGGATGAGAAAACAAAGAAATACTGTAATCCATTTGTTAAACCAAATCAGCCTCCTCCAGCAGGGATTTATAATATGAATGTGAGCACATCCGTCTCAGGTGAAAAGTACCTCCTTCAGGCAAACAAGAAAAGGAAGGAATATCCCAAAGCAGACGTGCGGTTGCCTGAACTAAACTATAACCATCTTCCTGAACTGAGAGCTTTAGAAGGCATAGCTCGAAATTCTAGGCTAATAAAGAAAGAGAACAAATGCCTTTCAGAATCTCGAATTCCCTCTCTGGCTGCCATTGATCTGCACGTGTCCAGTGTTGCATCACACCAG
Divergent primers for circular RNA PCR
Primer Set-1
Forward primer
Tm
Reverse primer
Tm
Product size
CCTCTCTGGCTGCCATTGAT
59.82
AGCTCTACTTCCTTTTTCCATT
55.34
146
Primer Set-2
Forward primer
Tm
Reverse primer
Tm
Product size
CCTCTCTGGCTGCCATTGAT
59.82
AAGCTCTACTTCCTTTTTCCAT
55.34
147
PCR template sequence:
TTCTAGGCTAATAAAGAAAGAGAACAAATGCCTTTCAGAATCTCGAATTCCCTCTCTGGCTGCCATTGATCTGCACGTGTCCAGTGTTGCATCACACCAGGATACCAATGCTGACCCCAAAATTAAGGATTCAAAAGTATTTAAAGTAAAGGGGTCAAAAATTGATGTTGAGAAAATGGAAAAAGGAAGTAGAGCTTCAA
Note: Users can design additional primers for provided template sequence using Primer3 or NCBI primer-blast.
miRNAs associated with circular RNAs
No of miRNAs
6
Interacting miRNAs (#binding sites)
mmu-miR-141-3p(1), mmu-miR-370-3p(1), mmu-miR-5101(1), mmu-miR-3470b(1), mmu-miR-338-3p(1), mmu-miR-181d-5p(1)
siRNAs for circular RNA silencing
Junction sequence
TGCATCACACCAGGATACCAATGCTG
siRNA sets
ATTGGTATCCTGGTGTGAT
Protein-coding potential of circular RNAs
CPAT analysis
CPAT ORF ID
CPAT Fickett
CPAT Hexamer
Coding probabilty
ORF length
CIRCCDKL2_621_ORF_1
1.0108
0.082557179
0.995351663
1167
ORF sequence:
ATGGAAAAAGGAAGTAGAGCTTCAAATGCCAACTGTCTCCATGACAATGGGACAAACCACAAAGGCTTGGCTTCCACCAGCCTCAGAGATTGCAGCAATGTCAACATTGATCACTCAAGGAACCCAGGCACAGCGATTCCTCCCCTCACACACAATCTTTCTGCAGTTGCTCCTGGCATTAATGCTGGAATGGGGACTATTCCTGGCGTTCAGAATTACAGAGTGGATGAGAAAACAAAGAAATACTGTAATCCATTTGTTAAACCAAATCAGCCTCCTCCAGCAGGGATTTATAATATGAATGTGAGCACATCCGTCTCAGGTGAAAAGTACCTCCTTCAGGCAAACAAGAAAAGGAAGGAATATCCCAAAGCAGACGTGCGGTTGCCTGAACTAAACTATAACCATCTTCCTGAACTGAGAGCTTTAGAAGGCATAGCTCGAAATTCTAGGCTAATAAAGAAAGAGAACAAATGCCTTTCAGAATCTCGAATTCCCTCTCTGGCTGCCATTGATCTGCACGTGTCCAGTGTTGCATCACACCAGGATACCAATGCTGACCCCAAAATTAAGGATTCAAAAGTATTTAAAGTAAAGGGGTCAAAAATTGATGTTGAGAAAATGGAAAAAGGAAGTAGAGCTTCAAATGCCAACTGTCTCCATGACAATGGGACAAACCACAAAGGCTTGGCTTCCACCAGCCTCAGAGATTGCAGCAATGTCAACATTGATCACTCAAGGAACCCAGGCACAGCGATTCCTCCCCTCACACACAATCTTTCTGCAGTTGCTCCTGGCATTAATGCTGGAATGGGGACTATTCCTGGCGTTCAGAATTACAGAGTGGATGAGAAAACAAAGAAATACTGTAATCCATTTGTTAAACCAAATCAGCCTCCTCCAGCAGGGATTTATAATATGAATGTGAGCACATCCGTCTCAGGTGAAAAGTACCTCCTTCAGGCAAACAAGAAAAGGAAGGAATATCCCAAAGCAGACGTGCGGTTGCCTGAACTAAACTATAACCATCTTCCTGAACTGAGAGCTTTAGAAGGCATAGCTCGAAATTCTAGGCTAATAAAGAAAGAGAACAAATGCCTTTCAGAATCTCGAATTCCCTCTCTGGCTGCCATTGATCTGCACGTGTCCAGTGTTGCATCACACCAG
Peptide sequence:
MEKGSRASNANCLHDNGTNHKGLASTSLRDCSNVNIDHSRNPGTAIPPLTHNLSAVAPGINAGMGTIPGVQNYRVDEKTKKYCNPFVKPNQPPPAGIYNMNVSTSVSGEKYLLQANKKRKEYPKADVRLPELNYNHLPELRALEGIARNSRLIKKENKCLSESRIPSLAAIDLHVSSVASHQDTNADPKIKDSKVFKVKGSKIDVEKMEKGSRASNANCLHDNGTNHKGLASTSLRDCSNVNIDHSRNPGTAIPPLTHNLSAVAPGINAGMGTIPGVQNYRVDEKTKKYCNPFVKPNQPPPAGIYNMNVSTSVSGEKYLLQANKKRKEYPKADVRLPELNYNHLPELRALEGIARNSRLIKKENKCLSESRIPSLAAIDLHVSSVASHQ
IRESfinder result
IRESfinder score
0.619736272
IRES/non IRES
IRES
riboCIRC information
riboCIRC ID
NA
NA
Evidence
Peptide sequence:
NA
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