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mmu_ciKdm1a_601
Basic information of circular RNA
PanCircBase ID:
mmu_ciKdm1a_601
mm39_Chr. Position ID:
chr4|136285882|136286483|-
Gene name:
Kdm1a
Transcript:
ENSMUST00000116273.9
CircRNA type:
Circular intronic (ci)RNA
Exon/Intron count:
1
Exon/intron indexes:
11
Exon/intron offsets:
0
Genomic length:
601
Exon/intron sizes in nt:
601
Flanking exon/introns:
chr4:136285882-136286483
Splice length:
601
Other database IDs:
Human Ortholog IDs:
Mature spliced Sequence:
GTCAGTGTCGGCCTGCCCTCAACAGTCAGGGAGAGGTAGGGAGCCTGAGCTGAGCCACAGCCAATGGCAACCGTCTGTACTAGGAGAAGGGGTTTGGTGCCTTAGGAGCCATGGAAAGTCAGTATTGTGTGAGAATGTTTCCTGCAGGATTCTTATCCTGACGGTTGAGATTGGTAATGCATGTGAAGTTTGAAGTCAGACTGTGGTTTAAATAACCCACCTGGTGTCCCTAACACCGTGGCCTCCTTAGTCACCTTGTCTGTGGCAGGCATGGTATTAGTCACACATAGCTTGGAGGGTCCTTGTGAAGCTTAAATGAACTGTATCTAAGGAGTCCTGTCCTAAGGCCCCGAGAGGTGCTGAGAGCATGGTAGCTGCTTTGCTCTACATCCTTGCTTGGAACACACTGCTAGTGCTTTTACCATTTCTCCTCCTGCCCTGTCTCACCCCAGACTCATAGCTTGTTTCCAGATAAAGAACCCCAGCCTTAAATTGAATCACACTTTATAAGCATGGTCTGAGCAGGAAGTGTGTTACATATGAATTAGGTAAATATCTATTTAAGATTAAGCCACACTCATTTATTTTTTTTATATGTCAG
Divergent primers for circular RNA PCR
Primer Set-1
Forward primer
Tm
Reverse primer
Tm
Product size
GCATGGTCTGAGCAGGAAGT
60.04
CTCAGGCTCCCTACCTCTCC
60.47
140
Primer Set-2
Forward primer
Tm
Reverse primer
Tm
Product size
AGCATGGTCTGAGCAGGAAG
59.75
CTCAGGCTCCCTACCTCTCC
60.47
141
PCR template sequence:
ACTTTATAAGCATGGTCTGAGCAGGAAGTGTGTTACATATGAATTAGGTAAATATCTATTTAAGATTAAGCCACACTCATTTATTTTTTTTATATGTCAGGTCAGTGTCGGCCTGCCCTCAACAGTCAGGGAGAGGTAGGGAGCCTGAGCTGAGCCACAGCCAATGGCAACCGTCTGTACTAGGAGAAGGGGTTTGGTGC
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-429-3p(1), mmu-miR-200b-3p(1), mmu-miR-216a-5p(1), mmu-miR-709(1), mmu-miR-24-3p(1), mmu-miR-494-3p(1), mmu-miR-411-3p(1), mmu-miR-342-3p(1), mmu-miR-377-3p(1), mmu-miR-207(1), mmu-miR-484(1), mmu-miR-670-5p(1)
siRNAs for circular RNA silencing
Junction sequence
TTTTATATGTCAGGTCAGTGTCGGCC
siRNA sets
NA
Protein-coding potential of circular RNAs
CPAT analysis
CPAT ORF ID
CPAT Fickett
CPAT Hexamer
Coding probabilty
ORF length
NA
NA
NA
NA
NA
ORF sequence:
NA
Peptide sequence:
NA
IRESfinder result
IRESfinder score
0.80095643
IRES/non IRES
IRES
riboCIRC information
riboCIRC ID
NA
NA
Evidence
Peptide sequence:
NA
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