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mmu_circArmc9_549

Basic information of circular RNA
PanCircBase ID:

mmu_circArmc9_549

mm39_Chr. Position ID:

chr1|86087716|86097724|+

Gene name:

Armc9

Transcript:

ENSMUST00000123618.8

CircRNA type:

Exonic circular (circ)RNA

Exon/Intron count:

4

Exon/intron indexes:

3,4,5,6

Exon/intron offsets:

0,2670,4701,9915

Genomic length:

10008

Exon/intron sizes in nt:

129,171,156,93

Flanking exon/introns:

chr1:86084727-86087716|chr1:86097724-86099845

Splice length:

549

Other database IDs:

Human Ortholog IDs:
Mature spliced Sequence:

TATTTAGATTTTGCTGAATTTGAAGACACCTTGAAGACATTTTCAAAAGAATGCAAAGTAAAAGGAAAGCCACTGTGTAAAAATGTCGGTGGGCCATTAAAGAAGGACTCCAAGTCGCTCGTAATCCAGAGGGATTTGGTGGCAGCGTTTGACAGTGGAGACCAGAAGGCGTTCTTTGACTTGTGGGAGGGGCACATTCCCAGCTCCGTCAGAGACACTGACTCCCTGGCCCAGAAGCTGGAGTTCTACCTTCACATCCACTTTGCCATCTACCTTCTCAAGTACTGCAGAGGCAGGCCGGACAAACAAGAGCTAGATAAAAGGATTTCTTATTTCAAAACCTACCTGGAGACAAAAGGGGCAGCGCTGAGCCAGACTACGGAGTTTCTGCCCTTCTATGCCCTCCCCTTCGTGCCCAATCCGATGGTCCACCCCTCATTTAAAGAACTCTTCCAGGATTCTTGGACTCCAGAATTAAAGCTGAAGCTGGAAAAGTTTTTAGCTTTAACTTTTAAAGCCAATAACACACCAAAGCTTTTAACCATATAT

Divergent primers for circular RNA PCR

Primer Set-1

Forward primer
Tm
Reverse primer
Tm
Product size

GCTGAAGCTGGAAAAGTTTTTAGC

59.55

GGCCCACCGACATTTTTACAC

60.07

165

Primer Set-2

Forward primer
Tm
Reverse primer
Tm
Product size

GCTGAAGCTGGAAAAGTTTTTAGC

59.55

GGCCCACCGACATTTTTACA

58.75

165

PCR template sequence:

CTTCCAGGATTCTTGGACTCCAGAATTAAAGCTGAAGCTGGAAAAGTTTTTAGCTTTAACTTTTAAAGCCAATAACACACCAAAGCTTTTAACCATATATTATTTAGATTTTGCTGAATTTGAAGACACCTTGAAGACATTTTCAAAAGAATGCAAAGTAAAAGGAAAGCCACTGTGTAAAAATGTCGGTGGGCCATTAA

Note: Users can design additional primers for provided template sequence using Primer3 or NCBI primer-blast.
miRNAs associated with circular RNAs
No of miRNAs

4

Interacting miRNAs (#binding sites)

mmu-miR-24-3p(1), mmu-miR-149-5p(1), mmu-miR-5101(1), mmu-miR-188-3p(1)

siRNAs for circular RNA silencing
Junction sequence

TTTAACCATATATTATTTAGATTTTG

siRNA sets

AAATCTAAATAATATATGG, AAAATCTAAATAATATATG, AATCTAAATAATATATGGT

Protein-coding potential of circular RNAs

CPAT analysis

CPAT ORF ID
CPAT Fickett
CPAT Hexamer
Coding probabilty
ORF length

CIRCARMC9_549_ORF_1

0.9181

0.118475725

0.857413616

675

ORF sequence:

ATGGTCCACCCCTCATTTAAAGAACTCTTCCAGGATTCTTGGACTCCAGAATTAAAGCTGAAGCTGGAAAAGTTTTTAGCTTTAACTTTTAAAGCCAATAACACACCAAAGCTTTTAACCATATATTATTTAGATTTTGCTGAATTTGAAGACACCTTGAAGACATTTTCAAAAGAATGCAAAGTAAAAGGAAAGCCACTGTGTAAAAATGTCGGTGGGCCATTAAAGAAGGACTCCAAGTCGCTCGTAATCCAGAGGGATTTGGTGGCAGCGTTTGACAGTGGAGACCAGAAGGCGTTCTTTGACTTGTGGGAGGGGCACATTCCCAGCTCCGTCAGAGACACTGACTCCCTGGCCCAGAAGCTGGAGTTCTACCTTCACATCCACTTTGCCATCTACCTTCTCAAGTACTGCAGAGGCAGGCCGGACAAACAAGAGCTAGATAAAAGGATTTCTTATTTCAAAACCTACCTGGAGACAAAAGGGGCAGCGCTGAGCCAGACTACGGAGTTTCTGCCCTTCTATGCCCTCCCCTTCGTGCCCAATCCGATGGTCCACCCCTCATTTAAAGAACTCTTCCAGGATTCTTGGACTCCAGAATTAAAGCTGAAGCTGGAAAAGTTTTTAGCTTTAACTTTTAAAGCCAATAACACACCAAAGCTTTTAACCATATAT

Peptide sequence:

MVHPSFKELFQDSWTPELKLKLEKFLALTFKANNTPKLLTIYYLDFAEFEDTLKTFSKECKVKGKPLCKNVGGPLKKDSKSLVIQRDLVAAFDSGDQKAFFDLWEGHIPSSVRDTDSLAQKLEFYLHIHFAIYLLKYCRGRPDKQELDKRISYFKTYLETKGAALSQTTEFLPFYALPFVPNPMVHPSFKELFQDSWTPELKLKLEKFLALTFKANNTPKLLTIY

IRESfinder result

IRESfinder score

0.698052864

IRES/non IRES

IRES

riboCIRC information

riboCIRC ID

NA

NA

Evidence
Peptide sequence:

NA

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