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mmu_circSh3pxd2a_206
Basic information of circular RNA
PanCircBase ID:
mmu_circSh3pxd2a_206
mm39_Chr. Position ID:
chr19|47302473|47331907|-
Gene name:
Sh3pxd2a
Transcript:
ENSMUST00000081619.10
CircRNA type:
Exonic circular (circ)RNA
Exon/Intron count:
3
Exon/intron indexes:
8,7,6
Exon/intron offsets:
0,6241,29405
Genomic length:
29434
Exon/intron sizes in nt:
132,45,29
Flanking exon/introns:
chr19:47275157-47302473|chr19:47331907-47353061
Splice length:
206
Other database IDs:
Human Ortholog IDs:
Mature spliced Sequence:
AGACTATGGCAGTTCCAAGAGGAAATCAGTGTGGTTGTCCAGCTGGGCTGAGTCTCCCAAGAAGGACGTGACAGGTGCCGACACCAACGCCGAGCCCATGATCCTGGAACAGTACGTGGTGGTGTCCAACTATAAGAAACAAGAGAACTCGGAGCTGAGCCTCCAGGCCGGGGAGGTGGTAGATGTCATCGAGAAGAACGAAAGCG
Divergent primers for circular RNA PCR
Primer Set-1
Forward primer
Tm
Reverse primer
Tm
Product size
CAGTACGTGGTGGTGTCCAA
59.89
CAGCTGGACAACCACACTGA
60.18
142
Primer Set-2
Forward primer
Tm
Reverse primer
Tm
Product size
GTACGTGGTGGTGTCCAACT
59.89
CAGCTGGACAACCACACTGA
60.18
140
PCR template sequence:
GAACAGTACGTGGTGGTGTCCAACTATAAGAAACAAGAGAACTCGGAGCTGAGCCTCCAGGCCGGGGAGGTGGTAGATGTCATCGAGAAGAACGAAAGCGAGACTATGGCAGTTCCAAGAGGAAATCAGTGTGGTTGTCCAGCTGGGCTGAGTCTCCCAAGAAGGACGTGACAGGTGCCGACACCAACGCCGAGCCCATG
Note: Users can design additional primers for provided template sequence using Primer3 or NCBI primer-blast.
miRNAs associated with circular RNAs
No of miRNAs
1
Interacting miRNAs (#binding sites)
mmu-miR-24-3p(2)
siRNAs for circular RNA silencing
Junction sequence
AAGAACGAAAGCGAGACTATGGCAGT
siRNA sets
ATAGTCTCGCTTTCGTTCT, CATAGTCTCGCTTTCGTTC, TAGTCTCGCTTTCGTTCTT
Protein-coding potential of circular RNAs
CPAT analysis
CPAT ORF ID
CPAT Fickett
CPAT Hexamer
Coding probabilty
ORF length
CIRCSH3PXD2A_206_ORF_1
1.0331
0.329439148
0.334993034
180
ORF sequence:
ATGATCCTGGAACAGTACGTGGTGGTGTCCAACTATAAGAAACAAGAGAACTCGGAGCTGAGCCTCCAGGCCGGGGAGGTGGTAGATGTCATCGAGAAGAACGAAAGCGAGACTATGGCAGTTCCAAGAGGAAATCAGTGTGGTTGTCCAGCTGGGCTGAGTCTCCCAAGAAGGACGTGA
Peptide sequence:
MILEQYVVVSNYKKQENSELSLQAGEVVDVIEKNESETMAVPRGNQCGCPAGLSLPRRT
IRESfinder result
IRESfinder score
0.140996745
IRES/non IRES
non-IRES
riboCIRC information
riboCIRC ID
NA
NA
Evidence
Peptide sequence:
NA
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