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mmu_circPdk3_489
Basic information of circular RNA
PanCircBase ID:
mmu_circPdk3_489
mm39_Chr. Position ID:
chrX|92843719|92857674|-
Gene name:
Pdk3
Transcript:
ENSMUST00000045748.7
CircRNA type:
Exonic circular (circ)RNA
Exon/Intron count:
4
Exon/intron indexes:
5,4,3,2
Exon/intron offsets:
0,2095,8757,13813
Genomic length:
13955
Exon/intron sizes in nt:
90,185,72,142
Flanking exon/introns:
chrX:92832577-92843719|chrX:92857674-92875452
Splice length:
489
Other database IDs:
circBase: mmu_circ_0016406, CIRCpedia: MMU_CIRCpedia_34612, circAtlas: mmu-Pdk3_0006
circBase: hsa_circ_0090135, circAtlas: hsa-PDK3_0001, CIRCpedia: HSA_CIRCpedia_65683
Human Ortholog IDs:
Mature spliced Sequence:
GAAGGGATAATGCATGTGAAAAAACTTCCTATATGTTTCTGCGCAAGGAACTTCCTGTGCGACTGGCTAACACCATGAGAGAGGTTAATCTCTTGCCGGATAACTTGTTGAACCGCCCTTCCGTGGGATTAGTTCAGAGCTGGTACATGCAGAGCTTCCTTGAACTTTTAGAATATGAAAACAAGAGCCCAGAAGACCCACGAGTTTTGGATAACTTTCTCAACGTTCTGATAAATATCAGAAACAGACACAATGATGTTGTTCCTACAATGGCCCAAGGCGTGATTGAGTACAAGGAAAAGTTCGGGTTTGATCCGTTCATTAGCAGTAACATTCAATATTTCCTGGATCGGTTTTATACCAACCGCATTTCTTTCCGCATGCTTATTAACCAGCACACACTTCTGTTTGGTGGTGACACTAACCCTGCACATCCGAAACATATAGGGAGTATCGACCCCACCTGTAATGTAGCTGATGTGGTTAAAG
Divergent primers for circular RNA PCR
Primer Set-1
Forward primer
Tm
Reverse primer
Tm
Product size
ACACTAACCCTGCACATCCG
60.04
TTAGCCAGTCGCACAGGAAG
60.04
142
Primer Set-2
Forward primer
Tm
Reverse primer
Tm
Product size
GGTGACACTAACCCTGCACA
59.89
TTAGCCAGTCGCACAGGAAG
60.04
146
PCR template sequence:
AACCAGCACACACTTCTGTTTGGTGGTGACACTAACCCTGCACATCCGAAACATATAGGGAGTATCGACCCCACCTGTAATGTAGCTGATGTGGTTAAAGGAAGGGATAATGCATGTGAAAAAACTTCCTATATGTTTCTGCGCAAGGAACTTCCTGTGCGACTGGCTAACACCATGAGAGAGGTTAATCTCTTGCCGGA
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-221-3p(1), mmu-miR-185-5p(1), mmu-miR-494-3p(1), mmu-miR-297a-5p(1), mmu-miR-323-3p(1)
siRNAs for circular RNA silencing
Junction sequence
GATGTGGTTAAAGGAAGGGATAATGC
siRNA sets
TATCCCTTCCTTTAACCAC, ATTATCCCTTCCTTTAACC, CATTATCCCTTCCTTTAAC
Protein-coding potential of circular RNAs
CPAT analysis
CPAT ORF ID
CPAT Fickett
CPAT Hexamer
Coding probabilty
ORF length
CIRCPDK3_489_ORF_1
1.0844
0.163174452
0.985757927
945
ORF sequence:
ATGTTTCTGCGCAAGGAACTTCCTGTGCGACTGGCTAACACCATGAGAGAGGTTAATCTCTTGCCGGATAACTTGTTGAACCGCCCTTCCGTGGGATTAGTTCAGAGCTGGTACATGCAGAGCTTCCTTGAACTTTTAGAATATGAAAACAAGAGCCCAGAAGACCCACGAGTTTTGGATAACTTTCTCAACGTTCTGATAAATATCAGAAACAGACACAATGATGTTGTTCCTACAATGGCCCAAGGCGTGATTGAGTACAAGGAAAAGTTCGGGTTTGATCCGTTCATTAGCAGTAACATTCAATATTTCCTGGATCGGTTTTATACCAACCGCATTTCTTTCCGCATGCTTATTAACCAGCACACACTTCTGTTTGGTGGTGACACTAACCCTGCACATCCGAAACATATAGGGAGTATCGACCCCACCTGTAATGTAGCTGATGTGGTTAAAGGAAGGGATAATGCATGTGAAAAAACTTCCTATATGTTTCTGCGCAAGGAACTTCCTGTGCGACTGGCTAACACCATGAGAGAGGTTAATCTCTTGCCGGATAACTTGTTGAACCGCCCTTCCGTGGGATTAGTTCAGAGCTGGTACATGCAGAGCTTCCTTGAACTTTTAGAATATGAAAACAAGAGCCCAGAAGACCCACGAGTTTTGGATAACTTTCTCAACGTTCTGATAAATATCAGAAACAGACACAATGATGTTGTTCCTACAATGGCCCAAGGCGTGATTGAGTACAAGGAAAAGTTCGGGTTTGATCCGTTCATTAGCAGTAACATTCAATATTTCCTGGATCGGTTTTATACCAACCGCATTTCTTTCCGCATGCTTATTAACCAGCACACACTTCTGTTTGGTGGTGACACTAACCCTGCACATCCGAAACATATAGGGAGTATCGACCCCACCTGTAATGTAGCTGATGTGGTTAAA
Peptide sequence:
MFLRKELPVRLANTMREVNLLPDNLLNRPSVGLVQSWYMQSFLELLEYENKSPEDPRVLDNFLNVLINIRNRHNDVVPTMAQGVIEYKEKFGFDPFISSNIQYFLDRFYTNRISFRMLINQHTLLFGGDTNPAHPKHIGSIDPTCNVADVVKGRDNACEKTSYMFLRKELPVRLANTMREVNLLPDNLLNRPSVGLVQSWYMQSFLELLEYENKSPEDPRVLDNFLNVLINIRNRHNDVVPTMAQGVIEYKEKFGFDPFISSNIQYFLDRFYTNRISFRMLINQHTLLFGGDTNPAHPKHIGSIDPTCNVADVVK
IRESfinder result
IRESfinder score
0.735278146
IRES/non IRES
IRES
riboCIRC information
riboCIRC ID
NA
NA
Evidence
Peptide sequence:
NA
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