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mmu_circAtm_497
Basic information of circular RNA
PanCircBase ID:
mmu_circAtm_497
mm39_Chr. Position ID:
chr9|53390880|53393743|-
Gene name:
Atm
Transcript:
ENSMUST00000118282.9
CircRNA type:
Exonic circular (circ)RNA
Exon/Intron count:
3
Exon/intron indexes:
36,35,34
Exon/intron offsets:
0,993,2721
Genomic length:
2863
Exon/intron sizes in nt:
17,81,77,142
Flanking exon/introns:
chr9:53385003-53390880|chr9:53393743-53395372
Splice length:
497
Other database IDs:
circAtlas: mmu-Atm_0006
circBase: hsa_circ_0005583, circAtlas: hsa-ATM_0005, CIRCpedia: HSA_CIRCpedia_3168
Human Ortholog IDs:
Mature spliced Sequence:
TGTCAAAATTCGATCTGCTGCTGCTACCTGTTTGAAAAACATTTTGGCTACAAAGATTGGACATATTTTCTGGGAGAATTATAAGACATCAGCGGATCCAATGCTGACCTATCTACAACCTTTTAGAACATCGAGGAAAAAGTTTTTAGAAGTGCCCCGATCTGTTAAAGAAGATGTTTTAGAAGGCCTGGATGCTGTGAATCTGTGGGTTCCTCAAAGTGAAAGTCATGACATTTGGATAAAGACACTGACGTGTGCCTTTCTGGACAGTGGAGGCATAAACAGTGAAATTCTCCAGTTATTAAAGCCAATGTGTGAAGTGAAAACCGACTTCTGTCAGATGTTGCTGCCATACTTGATCCATGATGTTTTACTGCAAGATACACATGAATCGTGGAGAACTCTGCTGTCTGCGCACGTCCGAGGATTTTTCACTAGTTGTTTTAAGCATTCCTCCCAAGCAAGCCGCTCAGCAACTCCTGCAAATTCGGATTCAG
Divergent primers for circular RNA PCR
Primer Set-1
Forward primer
Tm
Reverse primer
Tm
Product size
AGAACTCTGCTGTCTGCGC
60.37
TGTTTTTCAAACAGGTAGCAGCA
59.55
141
Primer Set-2
Forward primer
Tm
Reverse primer
Tm
Product size
AGCATTCCTCCCAAGCAAGC
60.97
TGGATCCGCTGATGTCTTAT
56.1
151
PCR template sequence:
AGAACTCTGCTGTCTGCGCACGTCCGAGGATTTTTCACTAGTTGTTTTAAGCATTCCTCCCAAGCAAGCCGCTCAGCAACTCCTGCAAATTCGGATTCAGTGTCAAAATTCGATCTGCTGCTGCTACCTGTTTGAAAAACATTTTGGCTACAAAGATTGGACATATTTTCTGGGAGAATTATAAGACATCAGCGGATCCA
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-124-3p(1), mmu-miR-16-5p(1), mmu-miR-15a-5p(1), mmu-miR-322-5p(1), mmu-miR-15b-5p(1), mmu-miR-673-5p(1)
siRNAs for circular RNA silencing
Junction sequence
AATTCGGATTCAGTGTCAAAATTCGA
siRNA sets
TTTTGACACTGAATCCGAA,TTTGACACTGAATCCGAAT
Protein-coding potential of circular RNAs
CPAT analysis
CPAT ORF ID
CPAT Fickett
CPAT Hexamer
Coding probabilty
ORF length
CIRCATM_497_ORF_1
0.7272
-0.006357838
0.305217894
432
ORF sequence:
ATGCTGACCTATCTACAACCTTTTAGAACATCGAGGAAAAAGTTTTTAGAAGTGCCCCGATCTGTTAAAGAAGATGTTTTAGAAGGCCTGGATGCTGTGAATCTGTGGGTTCCTCAAAGTGAAAGTCATGACATTTGGATAAAGACACTGACGTGTGCCTTTCTGGACAGTGGAGGCATAAACAGTGAAATTCTCCAGTTATTAAAGCCAATGTGTGAAGTGAAAACCGACTTCTGTCAGATGTTGCTGCCATACTTGATCCATGATGTTTTACTGCAAGATACACATGAATCGTGGAGAACTCTGCTGTCTGCGCACGTCCGAGGATTTTTCACTAGTTGTTTTAAGCATTCCTCCCAAGCAAGCCGCTCAGCAACTCCTGCAAATTCGGATTCAGTGTCAAAATTCGATCTGCTGCTGCTACCTGTTTGA
Peptide sequence:
MLTYLQPFRTSRKKFLEVPRSVKEDVLEGLDAVNLWVPQSESHDIWIKTLTCAFLDSGGINSEILQLLKPMCEVKTDFCQMLLPYLIHDVLLQDTHESWRTLLSAHVRGFFTSCFKHSSQASRSATPANSDSVSKFDLLLLPV
IRESfinder result
IRESfinder score
0.669328858
IRES/non IRES
IRES
riboCIRC information
riboCIRC ID
NA
NA
Evidence
Peptide sequence:
NA
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