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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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