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mmu_circPrkcsh_566
Basic information of circular RNA
PanCircBase ID:
mmu_circPrkcsh_566
mm39_Chr. Position ID:
chr9|21915793|21921898|+
Gene name:
Prkcsh
Transcript:
ENSMUST00000216344.2
CircRNA type:
Exonic circular (circ)RNA
Exon/Intron count:
6
Exon/intron indexes:
4,5,6,7,8,9
Exon/intron offsets:
0,193,2042,3746,5659,6026
Genomic length:
6105
Exon/intron sizes in nt:
96,58,118,130,85,79
Flanking exon/introns:
chr9:21915089-21915793|chr9:21921898-21922462
Splice length:
566
Other database IDs:
circBase: hsa_circ_0049466
Human Ortholog IDs:
Mature spliced Sequence:
GCACAGCTGCTTGTCCCAATGGCAGCTTTCACTGCACCAACACTGGGTACAAGCCCTTGTACATCCTCTCCAGCCGGGTCAATGATGGGGTATGTGACTGCTGTGATGGCACAGACGAGTACAACAGCGGCACGGTCTGCGAGAACACCTGCAGAGAGAAGGGTCGCAAGGAAAAAGAGTCCCTGCAGCAGCTGGCGGAAGTCACCCGTGAAGGGTTCCGCCTGAAGAAGATTCTCATTGAGGAGTGGAAGACAGCCCGGGAAGAAAAGCAGAGTAAGCTTCTTGAGCTTCAGGCTGGAAAGAAGTCTCTGGAAGACCAGGTAGAAACACTGCGGGCAGCGAAAGAAGAAGCAGAGAGGCCAGAGAAGGAGGCCAAGGACCAGCACCGGAAGCTGTGGGAAGAGCAGCAAGCTGCTGCCAAGGCCCGGCGGGAACAGGAGCGGGCAGCCAGTGCCTTCCAGGAACTTGACGACAACATGGATGGGATGGTCTCGCTGGCTGAGTTACAGACTCACCCGGAGCTGGACACAGATGGAGATGGAGCGCTGTCTGAGGAGGAGGCCCAG
Divergent primers for circular RNA PCR
Primer Set-1
Forward primer
Tm
Reverse primer
Tm
Product size
CATGGATGGGATGGTCTCGC
60.6
GGCTTGTACCCAGTGTTGGT
60.18
146
Primer Set-2
Forward primer
Tm
Reverse primer
Tm
Product size
CATGGATGGGATGGTCTCGC
60.6
GTACCCAGTGTTGGTGCAGT
60.18
141
PCR template sequence:
TGACGACAACATGGATGGGATGGTCTCGCTGGCTGAGTTACAGACTCACCCGGAGCTGGACACAGATGGAGATGGAGCGCTGTCTGAGGAGGAGGCCCAGGCACAGCTGCTTGTCCCAATGGCAGCTTTCACTGCACCAACACTGGGTACAAGCCCTTGTACATCCTCTCCAGCCGGGTCAATGATGGGGTATGTGACTG
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-34a-5p(1), mmu-miR-320-3p(1), mmu-miR-22-3p(1), mmu-miR-127-5p(1), mmu-miR-673-5p(1)
siRNAs for circular RNA silencing
Junction sequence
GGAGGAGGCCCAGGCACAGCTGCTTG
siRNA sets
NA
Protein-coding potential of circular RNAs
CPAT analysis
CPAT ORF ID
CPAT Fickett
CPAT Hexamer
Coding probabilty
ORF length
CIRCPRKCSH_566_ORF_1
1.0307
0.185373469
0.42024128
315
ORF sequence:
ATGGATGGGATGGTCTCGCTGGCTGAGTTACAGACTCACCCGGAGCTGGACACAGATGGAGATGGAGCGCTGTCTGAGGAGGAGGCCCAGGCACAGCTGCTTGTCCCAATGGCAGCTTTCACTGCACCAACACTGGGTACAAGCCCTTGTACATCCTCTCCAGCCGGGTCAATGATGGGGTATGTGACTGCTGTGATGGCACAGACGAGTACAACAGCGGCACGGTCTGCGAGAACACCTGCAGAGAGAAGGGTCGCAAGGAAAAAGAGTCCCTGCAGCAGCTGGCGGAAGTCACCCGTGAAGGGTTCCGCCTGA
Peptide sequence:
MDGMVSLAELQTHPELDTDGDGALSEEEAQAQLLVPMAAFTAPTLGTSPCTSSPAGSMMGYVTAVMAQTSTTAARSARTPAERRVARKKSPCSSWRKSPVKGSA
IRESfinder result
IRESfinder score
0.275824864
IRES/non IRES
non-IRES
riboCIRC information
riboCIRC ID
NA
NA
Evidence
Peptide sequence:
NA
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