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mmu_ciPkdcc_256
Basic information of circular RNA
PanCircBase ID:
mmu_ciPkdcc_256
mm39_Chr. Position ID:
chr17|83529298|83529554|+
Gene name:
Pkdcc
Transcript:
ENSMUST00000170794.8
CircRNA type:
Circular intronic (ci)RNA
Exon/Intron count:
1
Exon/intron indexes:
4
Exon/intron offsets:
0
Genomic length:
256
Exon/intron sizes in nt:
256
Flanking exon/introns:
chr17:83529298-83529554
Splice length:
256
Other database IDs:
Human Ortholog IDs:
Mature spliced Sequence:
GTAAGCCTCAGGACCCGTACACATCGGATTACCTGCCCCTGCCCTATCAGAAATAGGGACAAGCATGACCCTGGGACATGCAAGGTCTAGGACCCATTATATTCTAAGATAGTGTTCTGTGGTAAGGACCCTCCTTAGCCACCAAGTCCTGGCTTCGGGAAGGAAAGAGGGTGGCTTCCCATGGGAGGAATGGGAGTGGGAGCCAGGCATGTGGTGGTAACCGGGCATGTGGTAGTAACCATACCACACTTTGCAG
Divergent primers for circular RNA PCR
Primer Set-1
Forward primer
Tm
Reverse primer
Tm
Product size
CATGGGAGGAATGGGAGTGG
59.82
ATGTCCCAGGGTCATGCTTG
60.03
156
Primer Set-2
Forward primer
Tm
Reverse primer
Tm
Product size
CATGGGAGGAATGGGAGTGG
59.82
CATGTCCCAGGGTCATGCTT
60.03
157
PCR template sequence:
GGGAAGGAAAGAGGGTGGCTTCCCATGGGAGGAATGGGAGTGGGAGCCAGGCATGTGGTGGTAACCGGGCATGTGGTAGTAACCATACCACACTTTGCAGGTAAGCCTCAGGACCCGTACACATCGGATTACCTGCCCCTGCCCTATCAGAAATAGGGACAAGCATGACCCTGGGACATGCAAGGTCTAGGACCCATTAT
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-149-5p(1)
siRNAs for circular RNA silencing
Junction sequence
CCACACTTTGCAGGTAAGCCTCAGGA
siRNA sets
NA
Protein-coding potential of circular RNAs
CPAT analysis
CPAT ORF ID
CPAT Fickett
CPAT Hexamer
Coding probabilty
ORF length
CIPKDCC_256_ORF_1
1.0816
0.125359291
0.144476892
132
ORF sequence:
ATGGGAGGAATGGGAGTGGGAGCCAGGCATGTGGTGGTAACCGGGCATGTGGTAGTAACCATACCACACTTTGCAGGTAAGCCTCAGGACCCGTACACATCGGATTACCTGCCCCTGCCCTATCAGAAATAG
Peptide sequence:
MGGMGVGARHVVVTGHVVVTIPHFAGKPQDPYTSDYLPLPYQK
IRESfinder result
IRESfinder score
0.462971551
IRES/non IRES
non-IRES
riboCIRC information
riboCIRC ID
NA
NA
Evidence
Peptide sequence:
NA
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