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mmu_circPhtf2_366
Basic information of circular RNA
PanCircBase ID:
mmu_circPhtf2_366
mm39_Chr. Position ID:
chr5|21010652|21060199|-
Gene name:
Phtf2
Transcript:
ENSMUST00000118174.8
CircRNA type:
Exonic circular (circ)RNA
Exon/Intron count:
4
Exon/intron indexes:
5,4,3,2
Exon/intron offsets:
0,1749,7585,49467
Genomic length:
49547
Exon/intron sizes in nt:
159,70,57,80
Flanking exon/introns:
chr5:21008348-21010652|chr5:21060199-21086953
Splice length:
366
Other database IDs:
CIRCpedia: MMU_CIRCpedia_13056, circAtlas: mmu-Phtf2_0005
circBase: hsa_circ_0080871, circAtlas: hsa-SCAF8_0001, CIRCpedia: HSA_CIRCpedia_59046
Human Ortholog IDs:
Mature spliced Sequence:
CTTAAAATGACGAATGTGTGATCTCAATGGAATAAATGGCGTCCAGAGTCACAGATGCTATAGTCTGGTATCAGAAGAAGATTGGAGCCTATGATCAACAAATATGGGAAAAGTCTGTTGAACAAAGAGAAATCAAGGGCTTAAGGAATAAACCAAAGAAAACAGCACATGTGAAACCAGACCTCATCGATGTTGATCTTGTGAGAGGGTCTGCATTTGCTAAGGCAAAGCCTGAAAGTCCTTGGACTTCTCTGACAAGGAAAGGGATTGTTCGAGTTGTCTTTTTCCCTTTCTTCTCCCGCTGGTGGTTACAAGTAACGTCCAGAGTCATCTTCTCCTGGCTTCTTGTTCTCTATCTTCTCCAAG
Divergent primers for circular RNA PCR
Primer Set-1
Forward primer
Tm
Reverse primer
Tm
Product size
TTCCCTTTCTTCTCCCGCTG
59.68
AGCATCTGTGACTCTGGACG
59.47
141
Primer Set-2
Forward primer
Tm
Reverse primer
Tm
Product size
TTCCCTTTCTTCTCCCGCTG
59.68
GCATCTGTGACTCTGGACGC
61.08
140
PCR template sequence:
ATTGTTCGAGTTGTCTTTTTCCCTTTCTTCTCCCGCTGGTGGTTACAAGTAACGTCCAGAGTCATCTTCTCCTGGCTTCTTGTTCTCTATCTTCTCCAAGCTTAAAATGACGAATGTGTGATCTCAATGGAATAAATGGCGTCCAGAGTCACAGATGCTATAGTCTGGTATCAGAAGAAGATTGGAGCCTATGATCAACA
Note: Users can design additional primers for provided template sequence using Primer3 or NCBI primer-blast.
miRNAs associated with circular RNAs
No of miRNAs
3
Interacting miRNAs (#binding sites)
mmu-miR-29b-1-5p(1), mmu-miR-182-5p(1), mmu-miR-29b-2-5p(1)
siRNAs for circular RNA silencing
Junction sequence
TATCTTCTCCAAGCTTAAAATGACGA
siRNA sets
ATTTTAAGCTTGGAGAAGA, TTTTAAGCTTGGAGAAGAT, TTTAAGCTTGGAGAAGATA
Protein-coding potential of circular RNAs
CPAT analysis
CPAT ORF ID
CPAT Fickett
CPAT Hexamer
Coding probabilty
ORF length
CIRCPHTF2_366_ORF_1
0.706
-0.003633412
0.176898114
336
ORF sequence:
ATGGCGTCCAGAGTCACAGATGCTATAGTCTGGTATCAGAAGAAGATTGGAGCCTATGATCAACAAATATGGGAAAAGTCTGTTGAACAAAGAGAAATCAAGGGCTTAAGGAATAAACCAAAGAAAACAGCACATGTGAAACCAGACCTCATCGATGTTGATCTTGTGAGAGGGTCTGCATTTGCTAAGGCAAAGCCTGAAAGTCCTTGGACTTCTCTGACAAGGAAAGGGATTGTTCGAGTTGTCTTTTTCCCTTTCTTCTCCCGCTGGTGGTTACAAGTAACGTCCAGAGTCATCTTCTCCTGGCTTCTTGTTCTCTATCTTCTCCAAGCTTAA
Peptide sequence:
MASRVTDAIVWYQKKIGAYDQQIWEKSVEQREIKGLRNKPKKTAHVKPDLIDVDLVRGSAFAKAKPESPWTSLTRKGIVRVVFFPFFSRWWLQVTSRVIFSWLLVLYLLQA
IRESfinder result
IRESfinder score
0.64688615
IRES/non IRES
IRES
riboCIRC information
riboCIRC ID
NA
NA
Evidence
Peptide sequence:
NA
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