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mmu_circArmc9_866
Basic information of circular RNA
PanCircBase ID:
mmu_circArmc9_866
mm39_Chr. Position ID:
chr1|86087716|86113861|+
Gene name:
Armc9
Transcript:
ENSMUST00000123618.8
CircRNA type:
Exonic circular (circ)RNA
Exon/Intron count:
8
Exon/intron indexes:
3,4,5,6,7,8,9,10
Exon/intron offsets:
0,2670,4701,9915,12129,13562,16819,26110
Genomic length:
26145
Exon/intron sizes in nt:
129,171,156,93,25,158,99,35
Flanking exon/introns:
chr1:86084727-86087716|chr1:86113861-86116598
Splice length:
866
Other database IDs:
CIRCpedia: MMU_CIRCpedia_220585, circAtlas: mmu-Armc9_0018
Human Ortholog IDs:
Mature spliced Sequence:
TATTTAGATTTTGCTGAATTTGAAGACACCTTGAAGACATTTTCAAAAGAATGCAAAGTAAAAGGAAAGCCACTGTGTAAAAATGTCGGTGGGCCATTAAAGAAGGACTCCAAGTCGCTCGTAATCCAGAGGGATTTGGTGGCAGCGTTTGACAGTGGAGACCAGAAGGCGTTCTTTGACTTGTGGGAGGGGCACATTCCCAGCTCCGTCAGAGACACTGACTCCCTGGCCCAGAAGCTGGAGTTCTACCTTCACATCCACTTTGCCATCTACCTTCTCAAGTACTGCAGAGGCAGGCCGGACAAACAAGAGCTAGATAAAAGGATTTCTTATTTCAAAACCTACCTGGAGACAAAAGGGGCAGCGCTGAGCCAGACTACGGAGTTTCTGCCCTTCTATGCCCTCCCCTTCGTGCCCAATCCGATGGTCCACCCCTCATTTAAAGAACTCTTCCAGGATTCTTGGACTCCAGAATTAAAGCTGAAGCTGGAAAAGTTTTTAGCTTTAACTTTTAAAGCCAATAACACACCAAAGCTTTTAACCATATATAAGGAGAATGGACCTAATAGCAAAGAACTGCTGCAGCAGCTTCACCAGCAGCTGGTGGAGGCTGAGCGCCGGGCCATGACCTACCTGAAGCGGTACAATAAGATCCAAGCCGACTACCACAACCTCATCGGTGTCACAGCTGAGCTGGTGGACTCTCTGGAGGCCACAGTCAGCGGCAAGATGATCACCCCCGAGTACCTGCAGAGTGTCTGTGTCCGCCTCTTCAGTAACCAGATGCGGCAGAGCCTGGCACACAGCGTGGACTTCACGAGGCCTGGGACGGCCTCAACCATGTTGCGAGCCTCCTTGGCACCTGA
Divergent primers for circular RNA PCR
Primer Set-1
Forward primer
Tm
Reverse primer
Tm
Product size
GCACACAGCGTGGACTTCA
60.89
GGCCCACCGACATTTTTACAC
60.07
163
Primer Set-2
Forward primer
Tm
Reverse primer
Tm
Product size
CACACAGCGTGGACTTCAC
59.07
GGCCCACCGACATTTTTACAC
60.07
162
PCR template sequence:
GCCTCTTCAGTAACCAGATGCGGCAGAGCCTGGCACACAGCGTGGACTTCACGAGGCCTGGGACGGCCTCAACCATGTTGCGAGCCTCCTTGGCACCTGATATTTAGATTTTGCTGAATTTGAAGACACCTTGAAGACATTTTCAAAAGAATGCAAAGTAAAAGGAAAGCCACTGTGTAAAAATGTCGGTGGGCCATTAA
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-24-3p(1), mmu-miR-149-5p(1), mmu-miR-5101(1), mmu-miR-484(1), mmu-miR-188-3p(1), mmu-miR-3470b(1)
siRNAs for circular RNA silencing
Junction sequence
CCTTGGCACCTGATATTTAGATTTTG
siRNA sets
AAATCTAAATATCAGGTGC, AATCTAAATATCAGGTGCC, AAAATCTAAATATCAGGTG
Protein-coding potential of circular RNAs
CPAT analysis
CPAT ORF ID
CPAT Fickett
CPAT Hexamer
Coding probabilty
ORF length
CIRCARMC9_866_ORF_1
1.2407
0.401022278
0.871089805
450
ORF sequence:
ATGGTCCACCCCTCATTTAAAGAACTCTTCCAGGATTCTTGGACTCCAGAATTAAAGCTGAAGCTGGAAAAGTTTTTAGCTTTAACTTTTAAAGCCAATAACACACCAAAGCTTTTAACCATATATAAGGAGAATGGACCTAATAGCAAAGAACTGCTGCAGCAGCTTCACCAGCAGCTGGTGGAGGCTGAGCGCCGGGCCATGACCTACCTGAAGCGGTACAATAAGATCCAAGCCGACTACCACAACCTCATCGGTGTCACAGCTGAGCTGGTGGACTCTCTGGAGGCCACAGTCAGCGGCAAGATGATCACCCCCGAGTACCTGCAGAGTGTCTGTGTCCGCCTCTTCAGTAACCAGATGCGGCAGAGCCTGGCACACAGCGTGGACTTCACGAGGCCTGGGACGGCCTCAACCATGTTGCGAGCCTCCTTGGCACCTGATATTTAG
Peptide sequence:
MVHPSFKELFQDSWTPELKLKLEKFLALTFKANNTPKLLTIYKENGPNSKELLQQLHQQLVEAERRAMTYLKRYNKIQADYHNLIGVTAELVDSLEATVSGKMITPEYLQSVCVRLFSNQMRQSLAHSVDFTRPGTASTMLRASLAPDI
IRESfinder result
IRESfinder score
0.562756496
IRES/non IRES
IRES
riboCIRC information
riboCIRC ID
NA
NA
Evidence
Peptide sequence:
NA
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