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mmu_circClpx_357
Basic information of circular RNA
PanCircBase ID:
mmu_circClpx_357
mm39_Chr. Position ID:
chr9|65215749|65219421|+
Gene name:
Clpx
Transcript:
ENSMUST00000015501.11
CircRNA type:
Exonic circular (circ)RNA
Exon/Intron count:
3
Exon/intron indexes:
4,5,6
Exon/intron offsets:
0,1684,3630
Genomic length:
3672
Exon/intron sizes in nt:
155,160,42
Flanking exon/introns:
chr9:65209247-65215749|chr9:65219421-65223925
Splice length:
357
Other database IDs:
CIRCpedia: HSA_CIRCpedia_156488
Human Ortholog IDs:
Mature spliced Sequence:
CTTCCACGCGTTTTGTTAAGTGTGAAAAATGTCATCATTTTTTTGTGGTGCTGTCGGAAGCAGACTCAAAGAAAAGCATAATTAAGGAACCCGAGTCCGCTGCAGAGGCTGTGAAGTTGGCATTCCAGCAGAAGCCACCTCCGCCCCCCAAAAAGATTTATAACTACCTCGACAAGTATGTTGTTGGCCAGTCGTTTGCTAAGAAAGTGCTTTCAGTTGCCGTGTATAATCATTATAAGAGAATATATAATAATATTCCAGCTAATCTGAGACAGCAAGCAGAGGCTGAGAAGCAGACATCACTAACACCTAGAGAGTTAGAAATAAGAAGACGGGAGGATGAGTACAGATTTACAA
Divergent primers for circular RNA PCR
Primer Set-1
Forward primer
Tm
Reverse primer
Tm
Product size
TCTGAGACAGCAAGCAGAGG
59.39
TTGAGTCTGCTTCCGACAGC
60.32
161
Primer Set-2
Forward primer
Tm
Reverse primer
Tm
Product size
TGAGACAGCAAGCAGAGGC
60
TTGAGTCTGCTTCCGACAGC
60.32
159
PCR template sequence:
CCAGCTAATCTGAGACAGCAAGCAGAGGCTGAGAAGCAGACATCACTAACACCTAGAGAGTTAGAAATAAGAAGACGGGAGGATGAGTACAGATTTACAACTTCCACGCGTTTTGTTAAGTGTGAAAAATGTCATCATTTTTTTGTGGTGCTGTCGGAAGCAGACTCAAAGAAAAGCATAATTAAGGAACCCGAGTCCGC
Note: Users can design additional primers for provided template sequence using Primer3 or NCBI primer-blast.
miRNAs associated with circular RNAs
No of miRNAs
9
Interacting miRNAs (#binding sites)
mmu-let-7b-5p(1), mmu-let-7c-5p(1), mmu-miR-29b-3p(1), mmu-miR-29a-3p(1), mmu-miR-29c-3p(1), mmu-miR-196a-5p(1), mmu-miR-98-5p(1), mmu-miR-673-5p(1), mmu-miR-193b-3p(1)
siRNAs for circular RNA silencing
Junction sequence
TACAGATTTACAACTTCCACGCGTTT
siRNA sets
AAACGCGTGGAAGTTGTAA
Protein-coding potential of circular RNAs
CPAT analysis
CPAT ORF ID
CPAT Fickett
CPAT Hexamer
Coding probabilty
ORF length
CIRCCLPX_357_ORF_1
0.5203
-0.334276435
0.007071784
99
ORF sequence:
ATGAGTACAGATTTACAACTTCCACGCGTTTTGTTAAGTGTGAAAAATGTCATCATTTTTTTGTGGTGCTGTCGGAAGCAGACTCAAAGAAAAGCATAA
Peptide sequence:
MSTDLQLPRVLLSVKNVIIFLWCCRKQTQRKA
IRESfinder result
IRESfinder score
0.573253429
IRES/non IRES
IRES
riboCIRC information
riboCIRC ID
NA
NA
Evidence
Peptide sequence:
NA
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