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mmu_circPrkdc_414
Basic information of circular RNA
PanCircBase ID:
mmu_circPrkdc_414
mm39_Chr. Position ID:
chr16|15605008|15608538|+
Gene name:
Prkdc
Transcript:
ENSMUST00000023352.9
CircRNA type:
Exonic circular (circ)RNA
Exon/Intron count:
2
Exon/intron indexes:
65,66
Exon/intron offsets:
0,3305
Genomic length:
3530
Exon/intron sizes in nt:
1,89,225
Flanking exon/introns:
chr16:15603912-15605008|chr16:15608538-15609736
Splice length:
414
Other database IDs:
CIRCpedia: MMU_CIRCpedia_223681
circAtlas: hsa-SCAF8_0001
Human Ortholog IDs:
Mature spliced Sequence:
GCTTTAAATAAACTGGAGTGGGTGGATGGTGAACCCACAGAAGCTGAGAAGGAGTTTTGGGAGCTGGCATCGCTTGACTGTTACAACAACCTCTCTAAATGGAAAGAACTTGAGTACTGTTCTACAGTCAATATAGTCAGTGAGAACTCTCTTGACCTAAGTAAAATGTGGAGTGAACCATTTTATCAGGAGACGTATCTGCCATATGTGATCCGTAGCAAACTAAAGCTCCTGCTTCAAGGAGAAGGCAACCAATCTCTGCTAACATTTGTGGATGAAGCCATGAACAAGGAGCTGCAGAAGACGGTCCTGGAGCTTCAGTATAGTCAAGAGCTGAGTCTTCTTTACATCTTGCAGGATGATATTGACAGAGCCACATACTACATTAAAAATGGCATTCAGATTTTCATGCAA
Divergent primers for circular RNA PCR
Primer Set-1
Forward primer
Tm
Reverse primer
Tm
Product size
GCAGGATGATATTGACAGAGCC
58.93
TGTAACAGTCAAGCGATGCCA
60.27
146
Primer Set-2
Forward primer
Tm
Reverse primer
Tm
Product size
GCAGGATGATATTGACAGAGCC
58.93
GTAACAGTCAAGCGATGCCAG
59.61
145
PCR template sequence:
GCTTCAGTATAGTCAAGAGCTGAGTCTTCTTTACATCTTGCAGGATGATATTGACAGAGCCACATACTACATTAAAAATGGCATTCAGATTTTCATGCAAGCTTTAAATAAACTGGAGTGGGTGGATGGTGAACCCACAGAAGCTGAGAAGGAGTTTTGGGAGCTGGCATCGCTTGACTGTTACAACAACCTCTCTAAAT
Note: Users can design additional primers for provided template sequence using Primer3 or NCBI primer-blast.
miRNAs associated with circular RNAs
No of miRNAs
5
Interacting miRNAs (#binding sites)
mmu-miR-150-5p(1), mmu-miR-135a-5p(1), mmu-miR-132-3p(1), mmu-miR-127-5p(1), mmu-miR-194-5p(1)
siRNAs for circular RNA silencing
Junction sequence
GATTTTCATGCAAGCTTTAAATAAAC
siRNA sets
TTTATTTAAAGCTTGCATG, TTATTTAAAGCTTGCATGA, TATTTAAAGCTTGCATGAA
Protein-coding potential of circular RNAs
CPAT analysis
CPAT ORF ID
CPAT Fickett
CPAT Hexamer
Coding probabilty
ORF length
CIRCPRKDC_414_ORF_1
1.2609
0.27104672
0.95143136
663
ORF sequence:
ATGTGGAGTGAACCATTTTATCAGGAGACGTATCTGCCATATGTGATCCGTAGCAAACTAAAGCTCCTGCTTCAAGGAGAAGGCAACCAATCTCTGCTAACATTTGTGGATGAAGCCATGAACAAGGAGCTGCAGAAGACGGTCCTGGAGCTTCAGTATAGTCAAGAGCTGAGTCTTCTTTACATCTTGCAGGATGATATTGACAGAGCCACATACTACATTAAAAATGGCATTCAGATTTTCATGCAAGCTTTAAATAAACTGGAGTGGGTGGATGGTGAACCCACAGAAGCTGAGAAGGAGTTTTGGGAGCTGGCATCGCTTGACTGTTACAACAACCTCTCTAAATGGAAAGAACTTGAGTACTGTTCTACAGTCAATATAGTCAGTGAGAACTCTCTTGACCTAAGTAAAATGTGGAGTGAACCATTTTATCAGGAGACGTATCTGCCATATGTGATCCGTAGCAAACTAAAGCTCCTGCTTCAAGGAGAAGGCAACCAATCTCTGCTAACATTTGTGGATGAAGCCATGAACAAGGAGCTGCAGAAGACGGTCCTGGAGCTTCAGTATAGTCAAGAGCTGAGTCTTCTTTACATCTTGCAGGATGATATTGACAGAGCCACATACTACATTAAAAATGGCATTCAGATTTTCATGCAA
Peptide sequence:
MWSEPFYQETYLPYVIRSKLKLLLQGEGNQSLLTFVDEAMNKELQKTVLELQYSQELSLLYILQDDIDRATYYIKNGIQIFMQALNKLEWVDGEPTEAEKEFWELASLDCYNNLSKWKELEYCSTVNIVSENSLDLSKMWSEPFYQETYLPYVIRSKLKLLLQGEGNQSLLTFVDEAMNKELQKTVLELQYSQELSLLYILQDDIDRATYYIKNGIQIFMQ
IRESfinder result
IRESfinder score
0.669755766
IRES/non IRES
IRES
riboCIRC information
riboCIRC ID
NA
NA
Evidence
Peptide sequence:
NA
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