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mmu_circNpas3_412
Basic information of circular RNA
PanCircBase ID:
mmu_circNpas3_412
mm39_Chr. Position ID:
chr12|53401127|53687319|+
Gene name:
Npas3
Transcript:
ENSMUST00000101432.3
CircRNA type:
Exonic circular (circ)RNA
Exon/Intron count:
3
Exon/intron indexes:
2,3,4
Exon/intron offsets:
0,146689,286115
Genomic length:
286192
Exon/intron sizes in nt:
90,245,77
Flanking exon/introns:
chr12:53295530-53401127|chr12:53687319-53878478
Splice length:
412
Other database IDs:
CIRCpedia: HSA_CIRCpedia_120876
Human Ortholog IDs:
Mature spliced Sequence:
AATAACTGCCCAGCATCCTCTGCCCAACCAATCAGAATGTAGGAAAATCTACAGATATGACGGAATCTACTGTGAATCTACCTACCAGAATTTACAAGCACTGAGAAAGGAGAAATCCAGAGATGCTGCTCGATCCCGCCGGGGAAAAGAAAATTTTGAGTTCTATGAATTGGCCAAGCTGTTGCCTCTTCCTGCCGCCATCACCAGCCAGCTCGACAAGGCATCCATCATCCGACTTACAATTAGTTATCTCAAGATGAGAGACTTTGCCAACCAAGGGGATCCTCCATGGAACCTGAGGATGGAAGGCCCTCCACCAAACACCTCAGTAAAAGGTGCACAACGAAGGCGGAGCCCCAGCGCACTGGCCATTGAAGTATTTGAAGCACATTTGGGAAGCCACATTTTGCAG
Divergent primers for circular RNA PCR
Primer Set-1
Forward primer
Tm
Reverse primer
Tm
Product size
AAAAGGTGCACAACGAAGGC
59.9
GGTAGATTCACAGTAGATTCCGTCA
59.93
164
Primer Set-2
Forward primer
Tm
Reverse primer
Tm
Product size
AAAAGGTGCACAACGAAGGC
59.9
AGGTAGATTCACAGTAGATTCCGT
58.8
165
PCR template sequence:
TCCACCAAACACCTCAGTAAAAGGTGCACAACGAAGGCGGAGCCCCAGCGCACTGGCCATTGAAGTATTTGAAGCACATTTGGGAAGCCACATTTTGCAGAATAACTGCCCAGCATCCTCTGCCCAACCAATCAGAATGTAGGAAAATCTACAGATATGACGGAATCTACTGTGAATCTACCTACCAGAATTTACAAGCA
Note: Users can design additional primers for provided template sequence using Primer3 or NCBI primer-blast.
miRNAs associated with circular RNAs
No of miRNAs
5
Interacting miRNAs (#binding sites)
mmu-miR-15a-5p(1), mmu-miR-322-5p(1), mmu-miR-15b-5p(1), mmu-miR-298-5p(1), mmu-miR-138-5p(1)
siRNAs for circular RNA silencing
Junction sequence
CCACATTTTGCAGAATAACTGCCCAG
siRNA sets
NA
Protein-coding potential of circular RNAs
CPAT analysis
CPAT ORF ID
CPAT Fickett
CPAT Hexamer
Coding probabilty
ORF length
CIRCNPAS3_412_ORF_1
0.5767
0.051718585
0.072448954
198
ORF sequence:
ATGAGAGACTTTGCCAACCAAGGGGATCCTCCATGGAACCTGAGGATGGAAGGCCCTCCACCAAACACCTCAGTAAAAGGTGCACAACGAAGGCGGAGCCCCAGCGCACTGGCCATTGAAGTATTTGAAGCACATTTGGGAAGCCACATTTTGCAGAATAACTGCCCAGCATCCTCTGCCCAACCAATCAGAATGTAG
Peptide sequence:
MRDFANQGDPPWNLRMEGPPPNTSVKGAQRRRSPSALAIEVFEAHLGSHILQNNCPASSAQPIRM
IRESfinder result
IRESfinder score
0.472739823
IRES/non IRES
non-IRES
riboCIRC information
riboCIRC ID
NA
NA
Evidence
Peptide sequence:
NA
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