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mmu_circExosc9_564
Basic information of circular RNA
PanCircBase ID:
mmu_circExosc9_564
mm39_Chr. Position ID:
chr3|36608786|36616313|+
Gene name:
Exosc9
Transcript:
ENSMUST00000155866.8
CircRNA type:
Exonic circular (circ)RNA
Exon/Intron count:
5
Exon/intron indexes:
5,6,7,8,9
Exon/intron offsets:
0,844,2225,6465,7380
Genomic length:
7527
Exon/intron sizes in nt:
13,88,31,07,89,147
Flanking exon/introns:
chr3:36608291-36608786|chr3:36616313-36617221
Splice length:
564
Other database IDs:
circBase: mmu_circ_0010649, CIRCpedia: MMU_CIRCpedia_18125, circAtlas: mmu-Exosc9_0011
Human Ortholog IDs:
Mature spliced Sequence:
GTTTGGCAGATCCGTGTAGACCTACATTTATTAAATCATGATGGGAATATTATTGATGCTGCTAGCATTGCTGCAATTGTAGCCTTGTGTCACTTCCGAAGACCTGATGTCTCTGTCCAAGGAGAGGAAGTAACACTGTATACCCCTGAAGAGCGTGATCCCGTGCCATTGAGCATCCACCATATGCCCATTTGTGTCAGTTTTGCTTTCTTTCAGCAAGGAACATACTTATTGGTGGACCCCAATGAACGTGAAGAACGAGTAATGGATGGCTTGCTGGTGATTGCCATGAATAAGCATCGAGAAATTTGTACTATTCAGTCTAGTGGTTTTCAGATGCAGTAAAATAGCTGGTGTGAAAGTAGCAGAAATCACAGAGCTAATACAGAAAGCTTTGGAAAATGACCAGAGAGTCAGGAAAGAAGGTGGAAAATTTGGCTTTGCAGAGTCTATAGCAAACCAAAGAATCACAGCGTTTAAAATGGAGACGGCCCCTATTGATACCTCCAACATAGAGGAGAGAGCAGAAGAAATTATTGCTGAAGCTGAACCTCCCCCAGAAGT
Divergent primers for circular RNA PCR
Primer Set-1
Forward primer
Tm
Reverse primer
Tm
Product size
TGGAGACGGCCCCTATTGAT
60.4
ATTGCAGCAATGCTAGCAGC
59.9
159
Primer Set-2
Forward primer
Tm
Reverse primer
Tm
Product size
ATGGAGACGGCCCCTATTGA
60.4
ATTGCAGCAATGCTAGCAGC
59.9
160
PCR template sequence:
GAATCACAGCGTTTAAAATGGAGACGGCCCCTATTGATACCTCCAACATAGAGGAGAGAGCAGAAGAAATTATTGCTGAAGCTGAACCTCCCCCAGAAGTGTTTGGCAGATCCGTGTAGACCTACATTTATTAAATCATGATGGGAATATTATTGATGCTGCTAGCATTGCTGCAATTGTAGCCTTGTGTCACTTCCGAA
Note: Users can design additional primers for provided template sequence using Primer3 or NCBI primer-blast.
miRNAs associated with circular RNAs
No of miRNAs
7
Interacting miRNAs (#binding sites)
mmu-miR-9-5p(1), mmu-miR-16-5p(1), mmu-miR-15a-5p(1), mmu-miR-322-5p(1), mmu-miR-217-5p(1), mmu-miR-1904(1), mmu-miR-338-3p(1)
siRNAs for circular RNA silencing
Junction sequence
CTCCCCCAGAAGTGTTTGGCAGATCC
siRNA sets
NA
Protein-coding potential of circular RNAs
CPAT analysis
CPAT ORF ID
CPAT Fickett
CPAT Hexamer
Coding probabilty
ORF length
CIRCEXOSC9_564_ORF_3
1.0929
0.266939373
0.196295643
102
ORF sequence:
ATGGAGACGGCCCCTATTGATACCTCCAACATAGAGGAGAGAGCAGAAGAAATTATTGCTGAAGCTGAACCTCCCCCAGAAGTGTTTGGCAGATCCGTGTAG
Peptide sequence:
METAPIDTSNIEERAEEIIAEAEPPPEVFGRSV
IRESfinder result
IRESfinder score
0.619674255
IRES/non IRES
IRES
riboCIRC information
riboCIRC ID
NA
NA
Evidence
Peptide sequence:
NA
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