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mmu_circArmc9_1256
Basic information of circular RNA
PanCircBase ID:
mmu_circArmc9_1256
mm39_Chr. Position ID:
chr1|86101278|86172392|+
Gene name:
Armc9
Transcript:
ENSMUST00000135973.8
CircRNA type:
Exonic circular (circ)RNA
Exon/Intron count:
13
Exon/intron indexes:
8,9,10,11,12,13,14,15,16,17,18,19,20
Exon/intron offsets:
0,3257,12548,15320,17453,20720,22762,24685,26281,28933,34396,39493,71009
Genomic length:
71114
Exon/intron sizes in nt:
15,89,93,51,12,93,91,10,00,00,00,00,00,00,000
Flanking exon/introns:
chr1:86099870-86101278|chr1:86172392-86179998
Splice length:
1256
Other database IDs:
circAtlas: mmu-Armc9_0027
circAtlas: hsa-SCAF8_0001, CIRCpedia: HSA_CIRCpedia_40002
Human Ortholog IDs:
Mature spliced Sequence:
AACTGCTGCAGCAGCTTCACCAGCAGCTGGTGGAGGCTGAGCGCCGGGCCATGACCTACCTGAAGCGGTACAATAAGATCCAAGCCGACTACCACAACCTCATCGGTGTCACAGCTGAGCTGGTGGACTCTCTGGAGGCCACAGTCAGCGGCAAGATGATCACCCCCGAGTACCTGCAGAGTGTCTGTGTCCGCCTCTTCAGTAACCAGATGCGGCAGAGCCTGGCACACAGCGTGGACTTCACGAGGCCTGGGACGGCCTCAACCATGTTGCGAGCCTCCTTGGCACCTGAGAAGCTGAAGGATGTCCCGCTACTGCCCTCCCTGGATTATGAGAAGCTGAAGAAGGATTTGATCTGGGGGAGTGACCGCTTGAAAGCCTTCTTGTTGCAGGCTCTGCGCTGGCGCTTGACCACATCCCATCCGGGGGAGCAGAGGGAGACAGTCCTGCAAGCCTACATCAGCAATGACCTCTTGGATTGCCACAGCCATAACCAGAGGAGTGTGCTGCAGCTGCTGCACTCCAAGAGCGAGGCTGTGCGGCAGTACATGGCCAGGCTCATCAATGCCCTGGCGTCACTGGCTGAAGGTCGCCTGTACCTGGCCCAGAACACAAAGGTGCTGCGGATGCTGGAGGGAAGGCTCAAGGAGGAAGACAAGGATGTCATCACTCGTGAGAATGTCCTCGGGGCCTTGCAGAAGTTCAGCCTCAGGCGGCCACTGCAGACAGCGATGATTCGAGATGGCCTCATCTTCTGGCTGATCGACCTACTGAAGGACCCTGACTGCCTGTCTGACTACACATTGGAGTACTCCGTGGCTTTGCTCATGAACCTCTGCCTCCGCAGTGCAGGAAAGAACATGTGTGCTAAGGTGGCAGGGCTCATGCTGAAAGTTCTTTCGGATCTCCTTGGACACGAAAACCATGAGATCCAGCCGTATGTGAATGGAGCCCTGTACAGCATCCTCTCCATCCCGTCCATTCGAGAGGAGGCCAGAGCCATGGGAATGGAGGATATCCTGCGATGCTTCATCAAAGAAGGCAACGCTGAAATGATCCGCCAGATAGAGTTTATCATCAAGCAGCTGAATTCTGAAGATTTACTCGATGGTGTTCTTGAATCCGACGATGATGAAGATGAAGATGATGAAGAGGATCATGACATCATGGAAGCTGACCTGGACAAAGATGAACTGATCCAGCCCCAGCTGGGAGAACTCTCAGGCGAGAAGCTTCTAACCACAGAGTACTTGGGA
Divergent primers for circular RNA PCR
Primer Set-1
Forward primer
Tm
Reverse primer
Tm
Product size
CATGGAAGCTGACCTGGACA
59.67
CCGCTTCAGGTAGGTCATGG
60.18
159
Primer Set-2
Forward primer
Tm
Reverse primer
Tm
Product size
CATGGAAGCTGACCTGGACA
59.67
CTTCAGGTAGGTCATGGCCC
59.82
156
PCR template sequence:
TCATGACATCATGGAAGCTGACCTGGACAAAGATGAACTGATCCAGCCCCAGCTGGGAGAACTCTCAGGCGAGAAGCTTCTAACCACAGAGTACTTGGGAAACTGCTGCAGCAGCTTCACCAGCAGCTGGTGGAGGCTGAGCGCCGGGCCATGACCTACCTGAAGCGGTACAATAAGATCCAAGCCGACTACCACAACCT
Note: Users can design additional primers for provided template sequence using Primer3 or NCBI primer-blast.
miRNAs associated with circular RNAs
No of miRNAs
8
Interacting miRNAs (#binding sites)
mmu-miR-335-5p(1), mmu-miR-709(1), mmu-miR-511-3p(1), mmu-miR-484(1), mmu-miR-3470b(1), mmu-miR-697(1), mmu-miR-1904(1), mmu-miR-338-3p(1)
siRNAs for circular RNA silencing
Junction sequence
AGAGTACTTGGGAAACTGCTGCAGCA
siRNA sets
NA
Protein-coding potential of circular RNAs
CPAT analysis
CPAT ORF ID
CPAT Fickett
CPAT Hexamer
Coding probabilty
ORF length
CIRCARMC9_1256_ORF_1
1.3048
0.52087888
0.99976292
1260
ORF sequence:
ATGACCTACCTGAAGCGGTACAATAAGATCCAAGCCGACTACCACAACCTCATCGGTGTCACAGCTGAGCTGGTGGACTCTCTGGAGGCCACAGTCAGCGGCAAGATGATCACCCCCGAGTACCTGCAGAGTGTCTGTGTCCGCCTCTTCAGTAACCAGATGCGGCAGAGCCTGGCACACAGCGTGGACTTCACGAGGCCTGGGACGGCCTCAACCATGTTGCGAGCCTCCTTGGCACCTGAGAAGCTGAAGGATGTCCCGCTACTGCCCTCCCTGGATTATGAGAAGCTGAAGAAGGATTTGATCTGGGGGAGTGACCGCTTGAAAGCCTTCTTGTTGCAGGCTCTGCGCTGGCGCTTGACCACATCCCATCCGGGGGAGCAGAGGGAGACAGTCCTGCAAGCCTACATCAGCAATGACCTCTTGGATTGCCACAGCCATAACCAGAGGAGTGTGCTGCAGCTGCTGCACTCCAAGAGCGAGGCTGTGCGGCAGTACATGGCCAGGCTCATCAATGCCCTGGCGTCACTGGCTGAAGGTCGCCTGTACCTGGCCCAGAACACAAAGGTGCTGCGGATGCTGGAGGGAAGGCTCAAGGAGGAAGACAAGGATGTCATCACTCGTGAGAATGTCCTCGGGGCCTTGCAGAAGTTCAGCCTCAGGCGGCCACTGCAGACAGCGATGATTCGAGATGGCCTCATCTTCTGGCTGATCGACCTACTGAAGGACCCTGACTGCCTGTCTGACTACACATTGGAGTACTCCGTGGCTTTGCTCATGAACCTCTGCCTCCGCAGTGCAGGAAAGAACATGTGTGCTAAGGTGGCAGGGCTCATGCTGAAAGTTCTTTCGGATCTCCTTGGACACGAAAACCATGAGATCCAGCCGTATGTGAATGGAGCCCTGTACAGCATCCTCTCCATCCCGTCCATTCGAGAGGAGGCCAGAGCCATGGGAATGGAGGATATCCTGCGATGCTTCATCAAAGAAGGCAACGCTGAAATGATCCGCCAGATAGAGTTTATCATCAAGCAGCTGAATTCTGAAGATTTACTCGATGGTGTTCTTGAATCCGACGATGATGAAGATGAAGATGATGAAGAGGATCATGACATCATGGAAGCTGACCTGGACAAAGATGAACTGATCCAGCCCCAGCTGGGAGAACTCTCAGGCGAGAAGCTTCTAACCACAGAGTACTTGGGAAACTGCTGCAGCAGCTTCACCAGCAGCTGGTGGAGGCTGAGCGCCGGGCCATGA
Peptide sequence:
MTYLKRYNKIQADYHNLIGVTAELVDSLEATVSGKMITPEYLQSVCVRLFSNQMRQSLAHSVDFTRPGTASTMLRASLAPEKLKDVPLLPSLDYEKLKKDLIWGSDRLKAFLLQALRWRLTTSHPGEQRETVLQAYISNDLLDCHSHNQRSVLQLLHSKSEAVRQYMARLINALASLAEGRLYLAQNTKVLRMLEGRLKEEDKDVITRENVLGALQKFSLRRPLQTAMIRDGLIFWLIDLLKDPDCLSDYTLEYSVALLMNLCLRSAGKNMCAKVAGLMLKVLSDLLGHENHEIQPYVNGALYSILSIPSIREEARAMGMEDILRCFIKEGNAEMIRQIEFIIKQLNSEDLLDGVLESDDDEDEDDEEDHDIMEADLDKDELIQPQLGELSGEKLLTTEYLGNCCSSFTSSWWRLSAGP
IRESfinder result
IRESfinder score
0.248470244
IRES/non IRES
non-IRES
riboCIRC information
riboCIRC ID
NA
NA
Evidence
Peptide sequence:
NA
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