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mmu_circTop2a_159
Basic information of circular RNA
PanCircBase ID:
mmu_circTop2a_159
mm39_Chr. Position ID:
chr11|98891799|98891958|-
Gene name:
Top2a
Transcript:
ENSMUST00000068031.8
CircRNA type:
Exonic circular (circ)RNA
Exon/Intron count:
1
Exon/intron indexes:
26
Exon/intron offsets:
0
Genomic length:
159
Exon/intron sizes in nt:
159
Flanking exon/introns:
chr11:98891677-98891799|chr11:98891958-98892175
Splice length:
159
Other database IDs:
CIRCpedia: MMU_CIRCpedia_35986, circAtlas: mmu-Top2a_0021
Human Ortholog IDs:
Mature spliced Sequence:
GTTCCAGATGAAGAAGAAAATGAAGAAAGTGACACTGAAACCAGCACCAGTGACTCTGCAGCCGAGGCTGGGCCGACCTTCAACTACCTTCTCGACATGCCCCTGTGGTATCTGACCAAGGAGAAGAAGGATGAGCTGTGCAAACAAAGAAACGAGAAG
Divergent primers for circular RNA PCR
Primer Set-1
Forward primer
Tm
Reverse primer
Tm
Product size
CTACCTTCTCGACATGCCCC
59.89
CAGAGTCACTGGTGCTGGTT
59.89
134
Primer Set-2
Forward primer
Tm
Reverse primer
Tm
Product size
CTACCTTCTCGACATGCCCC
59.89
TGGTGCTGGTTTCAGTGTCA
59.75
125
PCR template sequence:
CAACTACCTTCTCGACATGCCCCTGTGGTATCTGACCAAGGAGAAGAAGGATGAGCTGTGCAAACAAAGAAACGAGAAGGTTCCAGATGAAGAAGAAAATGAAGAAAGTGACACTGAAACCAGCACCAGTGACTCTGCAGCCGAGGCTGGGCCGACCT
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-196a-5p(1), mmu-miR-29b-1-5p(1), mmu-miR-29b-2-5p(1), mmu-miR-207(1), mmu-miR-5101(1), mmu-miR-452-3p(1)
siRNAs for circular RNA silencing
Junction sequence
AAGAAACGAGAAGGTTCCAGATGAAG
siRNA sets
TTCATCTGGAACCTTCTCG, TCATCTGGAACCTTCTCGT, CTTCATCTGGAACCTTCTC
Protein-coding potential of circular RNAs
CPAT analysis
CPAT ORF ID
CPAT Fickett
CPAT Hexamer
Coding probabilty
ORF length
CIRCTOP2A_159_ORF_1
1.0432
0.526985156
0.609698837
222
ORF sequence:
ATGCCCCTGTGGTATCTGACCAAGGAGAAGAAGGATGAGCTGTGCAAACAAAGAAACGAGAAGGTTCCAGATGAAGAAGAAAATGAAGAAAGTGACACTGAAACCAGCACCAGTGACTCTGCAGCCGAGGCTGGGCCGACCTTCAACTACCTTCTCGACATGCCCCTGTGGTATCTGACCAAGGAGAAGAAGGATGAGCTGTGCAAACAAAGAAACGAGAAG
Peptide sequence:
MPLWYLTKEKKDELCKQRNEKVPDEEENEESDTETSTSDSAAEAGPTFNYLLDMPLWYLTKEKKDELCKQRNEK
IRESfinder result
IRESfinder score
0.336568947
IRES/non IRES
non-IRES
riboCIRC information
riboCIRC ID
NA
NA
Evidence
Peptide sequence:
NA
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