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mmu_circPrkdc_391
Basic information of circular RNA
PanCircBase ID:
mmu_circPrkdc_391
mm39_Chr. Position ID:
chr16|15653895|15656015|+
Gene name:
Prkdc
Transcript:
ENSMUST00000023352.9
CircRNA type:
Exonic circular (circ)RNA
Exon/Intron count:
2
Exon/intron indexes:
83,84
Exon/intron offsets:
0,1931
Genomic length:
2120
Exon/intron sizes in nt:
2,02,189
Flanking exon/introns:
chr16:15653825-15653895|chr16:15656015-15656948
Splice length:
391
Other database IDs:
CIRCpedia: MMU_CIRCpedia_212620
CIRCpedia: HSA_CIRCpedia_346269
Human Ortholog IDs:
Mature spliced Sequence:
GCGGGCCTTTGTAAAGATGAGCACCAGCCCTGAGGCCTTCCTGGCACTGCGTTCCCACTTTGCCAGCTCCCATGCACTGCTGTGCATCAGCCACTGGCTCCTCGGGATTGGAGACAGACACCTGAACAATTTCATGGTGGCCATGGAGACAGGCAGTGTGATTGGAATTGACTTTGGACATGCGTTTGGATCAGCTACTCAGTTTCTTCCAGTCCCTGAGTTGATGCCTTTTCGTCTAACCCGCCAATTTGTCAGTCTCATGTTGCCAATGAAAGAAACGGGTCTCATGTGCACGGTCATGGTGCATGCACTGAGGGCTTTCCGCTCTTGTGCAGGTCTGCTCACTGACACCATGGAAATTTTTGTGAAGGAACCCTCCTTTGATTGGAAG
Divergent primers for circular RNA PCR
Primer Set-1
Forward primer
Tm
Reverse primer
Tm
Product size
GTCATGGTGCATGCACTGAG
59.55
CAAAGTGGGAACGCAGTGC
60.01
158
Primer Set-2
Forward primer
Tm
Reverse primer
Tm
Product size
GTCATGGTGCATGCACTGAG
59.55
GCAAAGTGGGAACGCAGTG
60.01
159
PCR template sequence:
CACGGTCATGGTGCATGCACTGAGGGCTTTCCGCTCTTGTGCAGGTCTGCTCACTGACACCATGGAAATTTTTGTGAAGGAACCCTCCTTTGATTGGAAGGCGGGCCTTTGTAAAGATGAGCACCAGCCCTGAGGCCTTCCTGGCACTGCGTTCCCACTTTGCCAGCTCCCATGCACTGCTGTGCATCAGCCACTGGCTC
Note: Users can design additional primers for provided template sequence using Primer3 or NCBI primer-blast.
miRNAs associated with circular RNAs
No of miRNAs
4
Interacting miRNAs (#binding sites)
mmu-miR-152-3p(2), mmu-miR-148b-3p(1), mmu-miR-182-5p(1), mmu-miR-125b-1-3p(1)
siRNAs for circular RNA silencing
Junction sequence
CTTTGATTGGAAGGCGGGCCTTTGTA
siRNA sets
NA
Protein-coding potential of circular RNAs
CPAT analysis
CPAT ORF ID
CPAT Fickett
CPAT Hexamer
Coding probabilty
ORF length
CIRCPRKDC_391_ORF_1
1.0203
0.186410719
0.584776546
408
ORF sequence:
ATGAGCACCAGCCCTGAGGCCTTCCTGGCACTGCGTTCCCACTTTGCCAGCTCCCATGCACTGCTGTGCATCAGCCACTGGCTCCTCGGGATTGGAGACAGACACCTGAACAATTTCATGGTGGCCATGGAGACAGGCAGTGTGATTGGAATTGACTTTGGACATGCGTTTGGATCAGCTACTCAGTTTCTTCCAGTCCCTGAGTTGATGCCTTTTCGTCTAACCCGCCAATTTGTCAGTCTCATGTTGCCAATGAAAGAAACGGGTCTCATGTGCACGGTCATGGTGCATGCACTGAGGGCTTTCCGCTCTTGTGCAGGTCTGCTCACTGACACCATGGAAATTTTTGTGAAGGAACCCTCCTTTGATTGGAAGGCGGGCCTTTGTAAAGATGAGCACCAGCCCTGA
Peptide sequence:
MSTSPEAFLALRSHFASSHALLCISHWLLGIGDRHLNNFMVAMETGSVIGIDFGHAFGSATQFLPVPELMPFRLTRQFVSLMLPMKETGLMCTVMVHALRAFRSCAGLLTDTMEIFVKEPSFDWKAGLCKDEHQP
IRESfinder result
IRESfinder score
0.622592942
IRES/non IRES
IRES
riboCIRC information
riboCIRC ID
NA
NA
Evidence
Peptide sequence:
NA
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