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mmu_circPlekha8_601
Basic information of circular RNA
PanCircBase ID:
mmu_circPlekha8_601
mm39_Chr. Position ID:
chr6|54596178|54601623|+
Gene name:
Plekha8
Transcript:
ENSMUST00000119706.8
CircRNA type:
Exonic circular (circ)RNA
Exon/Intron count:
5
Exon/intron indexes:
5,6,7,8,9
Exon/intron offsets:
0,1078,2927,4881,5359
Genomic length:
5445
Exon/intron sizes in nt:
159,41,158,157,86
Flanking exon/introns:
chr6:54593742-54596178|chr6:54601623-54605830
Splice length:
601
Other database IDs:
circAtlas: mmu-Plekha8_0003
Human Ortholog IDs:
Mature spliced Sequence:
GAGGGAATTGATGTGGGAACCCTGCTAAAATCGACCTGCAACACTTTCCTGAAGACCTTGGAAGAATGCATGCAGATTGCAAACGCAGCCTTTACCTCCGAACTGCTTTACCATACACCCCCAGGGTCCCCTCAACTAGCGGTGCTTAAGTCCAGCAAGATGAAACATCCCATCATACCAATTCATAATTCGTTGGAAAGGTCGATGGAGTTAAACAGTTGTGAAAATGGATCGCTAAGTATAGAAGTAAATGGTGATGAAGAAATCCTAATGAAAACCAAGAGTTCCTTGTATTTGAAGTCCACAGAGGTGGATTGCAGCATCTCCAGTGAAGAAAACACAGATGACAATGTGACAGTCCAGGGGGAGATAATGAAGGAAGATGGCGAGGAAAACCTGGAGAGTCATGACAAGGATCCGGCACAGCCTGGATCAGACTCGGTTTGCTCGCCAGAATCTCCCTGGGAAGACAATGAAGAAGTTATTCCAACTTTCTTCAGTACTATGAATACCAGCTTTAGTGACATTGAACTTCTGGAGGACAGTGGCATTCCCACAGAAGCATTCTTGGCCTCCTGTTATGCAGTGGTTCCAGTCCTAG
Divergent primers for circular RNA PCR
Primer Set-1
Forward primer
Tm
Reverse primer
Tm
Product size
TGGCATTCCCACAGAAGCAT
59.96
GAGGTAAAGGCTGCGTTTGC
60.11
154
Primer Set-2
Forward primer
Tm
Reverse primer
Tm
Product size
CTGGAGGACAGTGGCATTCC
60.39
GAGGTAAAGGCTGCGTTTGC
60.11
165
PCR template sequence:
ACTATGAATACCAGCTTTAGTGACATTGAACTTCTGGAGGACAGTGGCATTCCCACAGAAGCATTCTTGGCCTCCTGTTATGCAGTGGTTCCAGTCCTAGGAGGGAATTGATGTGGGAACCCTGCTAAAATCGACCTGCAACACTTTCCTGAAGACCTTGGAAGAATGCATGCAGATTGCAAACGCAGCCTTTACCTCCG
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-miR-23b-3p(1), mmu-let-7b-5p(1), mmu-miR-217-5p(1), mmu-miR-320-3p(1), mmu-miR-23a-3p(1), mmu-miR-339-5p(1), mmu-miR-381-3p(1), mmu-miR-127-3p(1), mmu-miR-335-3p(1)
siRNAs for circular RNA silencing
Junction sequence
GTTCCAGTCCTAGGAGGGAATTGATG
siRNA sets
NA
Protein-coding potential of circular RNAs
CPAT analysis
CPAT ORF ID
CPAT Fickett
CPAT Hexamer
Coding probabilty
ORF length
CIRCPLEKHA8_601_ORF_1
0.952
0.18149593
0.761276474
543
ORF sequence:
ATGCAGATTGCAAACGCAGCCTTTACCTCCGAACTGCTTTACCATACACCCCCAGGGTCCCCTCAACTAGCGGTGCTTAAGTCCAGCAAGATGAAACATCCCATCATACCAATTCATAATTCGTTGGAAAGGTCGATGGAGTTAAACAGTTGTGAAAATGGATCGCTAAGTATAGAAGTAAATGGTGATGAAGAAATCCTAATGAAAACCAAGAGTTCCTTGTATTTGAAGTCCACAGAGGTGGATTGCAGCATCTCCAGTGAAGAAAACACAGATGACAATGTGACAGTCCAGGGGGAGATAATGAAGGAAGATGGCGAGGAAAACCTGGAGAGTCATGACAAGGATCCGGCACAGCCTGGATCAGACTCGGTTTGCTCGCCAGAATCTCCCTGGGAAGACAATGAAGAAGTTATTCCAACTTTCTTCAGTACTATGAATACCAGCTTTAGTGACATTGAACTTCTGGAGGACAGTGGCATTCCCACAGAAGCATTCTTGGCCTCCTGTTATGCAGTGGTTCCAGTCCTAGGAGGGAATTGA
Peptide sequence:
MQIANAAFTSELLYHTPPGSPQLAVLKSSKMKHPIIPIHNSLERSMELNSCENGSLSIEVNGDEEILMKTKSSLYLKSTEVDCSISSEENTDDNVTVQGEIMKEDGEENLESHDKDPAQPGSDSVCSPESPWEDNEEVIPTFFSTMNTSFSDIELLEDSGIPTEAFLASCYAVVPVLGGN
IRESfinder result
IRESfinder score
0.513966175
IRES/non IRES
IRES
riboCIRC information
riboCIRC ID
NA
NA
Evidence
Peptide sequence:
NA
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