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mmu_circPhf20_257
Basic information of circular RNA
PanCircBase ID:
mmu_circPhf20_257
mm39_Chr. Position ID:
chr2|156093695|156096230|+
Gene name:
Phf20
Transcript:
ENSMUST00000037401.10
CircRNA type:
Exonic circular (circ)RNA
Exon/Intron count:
2
Exon/intron indexes:
3,4
Exon/intron offsets:
0,2450
Genomic length:
2535
Exon/intron sizes in nt:
172,85
Flanking exon/introns:
chr2:156065369-156093695|chr2:156096230-156106200
Splice length:
257
Other database IDs:
circBase: mmu_circ_0009491, CIRCpedia: MMU_CIRCpedia_10721, circAtlas: mmu-Phf20_0003
circBase: hsa_circ_0005163, circAtlas: hsa-PHF20_0003, CIRCpedia: HSA_CIRCpedia_33979
Human Ortholog IDs:
Mature spliced Sequence:
GTATCCAGCTCATATTGAAGACATTGACTACGAAGAAGGGAGAGTTCTCATCCATTTCAAGCGTTGGAACCATCGTTACGATGAGTGGTTTTGCTGGGACAGTCCTTATCTGCGCCCTTTAGAGAAGATCCAGCTGAGGAAAGAGGGTTTACATGATGAGGATGGCTCTTCTGAATTTCAAATAAACCAGCAAGTGCTTGCTTGCTGGTCTGACTGTCGATTTTATCCAGCCAGAGTCACTGCTGTGAACAAGGATG
Divergent primers for circular RNA PCR
Primer Set-1
Forward primer
Tm
Reverse primer
Tm
Product size
TTGCTTGCTGGTCTGACTGT
59.82
CGTAACGATGGTTCCAACGC
59.91
140
Primer Set-2
Forward primer
Tm
Reverse primer
Tm
Product size
CAAGTGCTTGCTTGCTGGTC
60.32
CGTAACGATGGTTCCAACGC
59.91
147
PCR template sequence:
GAGGATGGCTCTTCTGAATTTCAAATAAACCAGCAAGTGCTTGCTTGCTGGTCTGACTGTCGATTTTATCCAGCCAGAGTCACTGCTGTGAACAAGGATGGTATCCAGCTCATATTGAAGACATTGACTACGAAGAAGGGAGAGTTCTCATCCATTTCAAGCGTTGGAACCATCGTTACGATGAGTGGTTTTGCTGGGAC
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-34a-5p(1), mmu-miR-203-3p(1), mmu-miR-29b-1-5p(1), mmu-miR-362-5p(1), mmu-miR-673-5p(1)
siRNAs for circular RNA silencing
Junction sequence
GTGAACAAGGATGGTATCCAGCTCAT
siRNA sets
NA
Protein-coding potential of circular RNAs
CPAT analysis
CPAT ORF ID
CPAT Fickett
CPAT Hexamer
Coding probabilty
ORF length
NA
NA
NA
NA
NA
ORF sequence:
NA
Peptide sequence:
NA
IRESfinder result
IRESfinder score
0.642372082
IRES/non IRES
IRES
riboCIRC information
riboCIRC ID
NA
NA
Evidence
Peptide sequence:
NA
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