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mmu_circPdk1_214
Basic information of circular RNA
PanCircBase ID:
mmu_circPdk1_214
mm39_Chr. Position ID:
chr2|71705749|71710454|+
Gene name:
Pdk1
Transcript:
ENSMUST00000006669.6
CircRNA type:
Exonic circular (circ)RNA
Exon/Intron count:
2
Exon/intron indexes:
2,3
Exon/intron offsets:
0,4633
Genomic length:
4705
Exon/intron sizes in nt:
142,72
Flanking exon/introns:
chr2:71703909-71705749|chr2:71710454-71713766
Splice length:
214
Other database IDs:
CIRCpedia: MMU_CIRCpedia_27925, circAtlas: mmu-Pdk1_0006
circBase: hsa_circ_0057087, circAtlas: hsa-SCAF8_0001, CIRCpedia: HSA_CIRCpedia_38638
Human Ortholog IDs:
Mature spliced Sequence:
GGTCAGTGAATGCTTGTGAAAAGACCTCGTTTATGTTTCTGCGACAAGAGTTGCCTGTTAGATTGGCAAATATAATGAAAGAAATCAGCCTCCTCCCCGACAATCTTCTCAGGACCCCATCCGTACAGCTGGTGCAAAGTTGGTATATCCAAAGCCTTCAGGAGTTGCTTGATTTTAAAGACAAAAGTGCTGAAGATGCTAAAACTATTTATGA
Divergent primers for circular RNA PCR
Primer Set-1
Forward primer
Tm
Reverse primer
Tm
Product size
ATCCGTACAGCTGGTGCAAA
59.96
GGCAACTCTTGTCGCAGAAA
59.06
151
Primer Set-2
Forward primer
Tm
Reverse primer
Tm
Product size
ATCCGTACAGCTGGTGCAAA
59.96
GCAACTCTTGTCGCAGAAACA
59.67
150
PCR template sequence:
CCCCATCCGTACAGCTGGTGCAAAGTTGGTATATCCAAAGCCTTCAGGAGTTGCTTGATTTTAAAGACAAAAGTGCTGAAGATGCTAAAACTATTTATGAGGTCAGTGAATGCTTGTGAAAAGACCTCGTTTATGTTTCTGCGACAAGAGTTGCCTGTTAGATTGGCAAATATAATGAAAGAAATCAGCCTCCTCCCCGA
Note: Users can design additional primers for provided template sequence using Primer3 or NCBI primer-blast.
miRNAs associated with circular RNAs
No of miRNAs
2
Interacting miRNAs (#binding sites)
mmu-miR-494-3p(1), mmu-miR-382-3p(1)
siRNAs for circular RNA silencing
Junction sequence
AAACTATTTATGAGGTCAGTGAATGC
siRNA sets
ATTCACTGACCTCATAAAT
Protein-coding potential of circular RNAs
CPAT analysis
CPAT ORF ID
CPAT Fickett
CPAT Hexamer
Coding probabilty
ORF length
CIRCPDK1_214_ORF_1
0.9959
-0.0182444
0.140793092
231
ORF sequence:
ATGCTAAAACTATTTATGAGGTCAGTGAATGCTTGTGAAAAGACCTCGTTTATGTTTCTGCGACAAGAGTTGCCTGTTAGATTGGCAAATATAATGAAAGAAATCAGCCTCCTCCCCGACAATCTTCTCAGGACCCCATCCGTACAGCTGGTGCAAAGTTGGTATATCCAAAGCCTTCAGGAGTTGCTTGATTTTAAAGACAAAAGTGCTGAAGATGCTAAAACTATTTAT
Peptide sequence:
MLKLFMRSVNACEKTSFMFLRQELPVRLANIMKEISLLPDNLLRTPSVQLVQSWYIQSLQELLDFKDKSAEDAKTIY
IRESfinder result
IRESfinder score
0.671085987
IRES/non IRES
IRES
riboCIRC information
riboCIRC ID
NA
NA
Evidence
Peptide sequence:
NA
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