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mmu_ciCkap5_436
Basic information of circular RNA
PanCircBase ID:
mmu_ciCkap5_436
mm39_Chr. Position ID:
chr2|91402878|91403314|+
Gene name:
Ckap5
Transcript:
ENSMUST00000111338.10
CircRNA type:
Circular intronic (ci)RNA
Exon/Intron count:
1
Exon/intron indexes:
17
Exon/intron offsets:
0
Genomic length:
436
Exon/intron sizes in nt:
436
Flanking exon/introns:
chr2:91402878-91403317
Splice length:
436
Other database IDs:
Human Ortholog IDs:
Mature spliced Sequence:
GTGAGTTCCAGAGCTGTCTCCCTGTGTTGTCCCAGGTTGTCCCCAATGTTAACTGAGGCCTACCAATCACAGTTAATTCTTGAGTATAGTTTTTTATAACTGTGGGGTCTTTGTGTATGTATATGCCCTGGCTGACCTGCAACTTACTATAGCAAATAACATTAATTTTCTTTTAAGACACTGTAATTCAAATGGATCAGTCAATGAAAGTTTCAAACAAGAATGTTTTAAAACTCTGCACCTCATTTCTTTTTAGGATAAATTAAGTCTTTTGTTAATAGATCCTTATACTTAACACCTAGAAACTCATATTTAATAAGTGACTTTAATATGCCTCATATTTAATATATGAATTTAAATTAAAGTCATAACTTATTTCTATGAGAAATATAAGAAAAGTAGAGATCTGATGCTATGTTTTCTGATGCTATTGTTT
Divergent primers for circular RNA PCR
Primer Set-1
Forward primer
Tm
Reverse primer
Tm
Product size
ATAAGAAAAGTAGAGATCTGATGCT
55.63
AAAACTATACTCAAGAATTAACTGTGA
55.37
140
Primer Set-2
Forward primer
Tm
Reverse primer
Tm
Product size
ATAAGAAAAGTAGAGATCTGATGCTA
55.59
AAAACTATACTCAAGAATTAACTGTGA
55.37
140
PCR template sequence:
CATATTTAATATATGAATTTAAATTAAAGTCATAACTTATTTCTATGAGAAATATAAGAAAAGTAGAGATCTGATGCTATGTTTTCTGATGCTATTGTTTGTGAGTTCCAGAGCTGTCTCCCTGTGTTGTCCCAGGTTGTCCCCAATGTTAACTGAGGCCTACCAATCACAGTTAATTCTTGAGTATAGTTTTTTATAAC
Note: Users can design additional primers for provided template sequence using Primer3 or NCBI primer-blast.
miRNAs associated with circular RNAs
No of miRNAs
3
Interacting miRNAs (#binding sites)
mmu-miR-466d-3p(1), mmu-miR-466b-3p(1), mmu-miR-350-3p(1)
siRNAs for circular RNA silencing
Junction sequence
GATGCTATTGTTTGTGAGTTCCAGAG
siRNA sets
AACTCACAAACAATAGCAT, GGAACTCACAAACAATAGC, GAACTCACAAACAATAGCA
Protein-coding potential of circular RNAs
CPAT analysis
CPAT ORF ID
CPAT Fickett
CPAT Hexamer
Coding probabilty
ORF length
CICKAP5_436_ORF_1
0.775
-0.469616896
0.007899202
126
ORF sequence:
ATGCTATGTTTTCTGATGCTATTGTTTGTGAGTTCCAGAGCTGTCTCCCTGTGTTGTCCCAGGTTGTCCCCAATGTTAACTGAGGCCTACCAATCACAGTTAATTCTTGAGTATAGTTTTTTATAA
Peptide sequence:
MLCFLMLLFVSSRAVSLCCPRLSPMLTEAYQSQLILEYSFL
IRESfinder result
IRESfinder score
0.94427268
IRES/non IRES
IRES
riboCIRC information
riboCIRC ID
NA
NA
Evidence
Peptide sequence:
NA
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