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mmu_circChka_114
Basic information of circular RNA
PanCircBase ID:
mmu_circChka_114
mm39_Chr. Position ID:
chr19|3921002|3925788|+
Gene name:
Chka
Transcript:
ENSMUST00000128694.8
CircRNA type:
Exonic circular (circ)RNA
Exon/Intron count:
2
Exon/intron indexes:
3,4
Exon/intron offsets:
0,4732
Genomic length:
4786
Exon/intron sizes in nt:
60,54
Flanking exon/introns:
chr19:3914759-3921002|chr19:3925788-3934471
Splice length:
114
Other database IDs:
CIRCpedia: MMU_CIRCpedia_212805, circAtlas: mmu-Chka_0011
Human Ortholog IDs:
Mature spliced Sequence:
GCTTGTCCATGCGATCGTGCCTGGAGCACTCTGGTTTCCAGGTGACAGACACGATTCACGAGGTCCTGTAATAAAGAGGGATCCGAACAAGCTCAGAATGAAAATGAATTTCAA
Divergent primers for circular RNA PCR
Primer Set-1
Forward primer
Tm
Reverse primer
Tm
Product size
GGGATCCGAACAAGCTCAGA
59.46
GGAAACCAGAGTGCTCCAGG
60.32
76
Primer Set-2
Forward primer
Tm
Reverse primer
Tm
Product size
GAGGGATCCGAACAAGCTCA
59.46
GGAAACCAGAGTGCTCCAGG
60.32
78
PCR template sequence:
ACGAGGTCCTGTAATAAAGAGGGATCCGAACAAGCTCAGAATGAAAATGAATTTCAAGCTTGTCCATGCGATCGTGCCTGGAGCACTCTGGTTTCCAGGTGACAGACACGATTC
Note: Users can design additional primers for provided template sequence using Primer3 or NCBI primer-blast.
miRNAs associated with circular RNAs
No of miRNAs
2
Interacting miRNAs (#binding sites)
mmu-miR-127-3p(1), mmu-miR-335-3p(1)
siRNAs for circular RNA silencing
Junction sequence
AAATGAATTTCAAGCTTGTCCATGCG
siRNA sets
ATGGACAAGCTTGAAATTC
Protein-coding potential of circular RNAs
CPAT analysis
CPAT ORF ID
CPAT Fickett
CPAT Hexamer
Coding probabilty
ORF length
CIRCCHKA_114_ORF_1
0.9612
0.027409066
0.08181117
129
ORF sequence:
ATGAAAATGAATTTCAAGCTTGTCCATGCGATCGTGCCTGGAGCACTCTGGTTTCCAGGTGACAGACACGATTCACGAGGTCCTGTAATAAAGAGGGATCCGAACAAGCTCAGAATGAAAATGAATTTC
Peptide sequence:
MKMNFKLVHAIVPGALWFPGDRHDSRGPVIKRDPNKLRMKMNF
IRESfinder result
IRESfinder score
0.646884021
IRES/non IRES
IRES
riboCIRC information
riboCIRC ID
NA
NA
Evidence
Peptide sequence:
NA
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