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mmu_circPhka1_540
Basic information of circular RNA
PanCircBase ID:
mmu_circPhka1_540
mm39_Chr. Position ID:
chrX|101664943|101685985|-
Gene name:
Phka1
Transcript:
ENSMUST00000043596.12
CircRNA type:
Exonic circular (circ)RNA
Exon/Intron count:
5
Exon/intron indexes:
6,5,4,3,2
Exon/intron offsets:
0,4250,15205,17743,20883
Genomic length:
21042
Exon/intron sizes in nt:
8,18,31,69,48,159
Flanking exon/introns:
chrX:101661021-101664943|chrX:101685985-101687452
Splice length:
540
Other database IDs:
circAtlas: mmu-Phka1_0027
Human Ortholog IDs:
Mature spliced Sequence:
AATCCAGTGACAGGCTTGCTTCCAGCCAGCTATGATCAAAAAGATGCCTGGGTCCGAGATAATGTGTACAGTATCCTGGCTGTGTGGGGTTTGGGCCTGGCATATCGCAAAAATGCTGACCGTGATGAGGACAAGGCAAAGGCCTATGAACTGGAGCAGAGTGTAGTGAAGTTAATGAGGGGACTGCTGCACTGCATGATCAGACAGGTGGATAAAGTAGAGTCCTTCAAGTACAGTCAGAGTACTAAAGATAGCCTCCATGCCAAGTACAACACCAAAACTTGTGCCACTGTGGTGGGTGATGACCAGTGGGGACACCTGCAGTTGGATGCTACTTCTGTGTACCTGCTCTTCCTAGCACAAATGACTGCCTCAGGACTCCATATCATCCACAGCCTAGACGAAGTCAATTTTATACAGAACCTCGTGTTTTACATTGAAGCTGCATATAAAACTGCTGACTTTGGGATATGGGAACGTGGCGATAAGACAAACCAAGGCATCTCGGAATTGAATGCGAGTTCAGTTGGAATGGCCAAG
Divergent primers for circular RNA PCR
Primer Set-1
Forward primer
Tm
Reverse primer
Tm
Product size
TTGGGATATGGGAACGTGGC
60.11
CATTATCTCGGACCCAGGCA
59.24
141
Primer Set-2
Forward primer
Tm
Reverse primer
Tm
Product size
TTGGGATATGGGAACGTGGC
60.11
ACATTATCTCGGACCCAGGC
59.24
142
PCR template sequence:
AGCTGCATATAAAACTGCTGACTTTGGGATATGGGAACGTGGCGATAAGACAAACCAAGGCATCTCGGAATTGAATGCGAGTTCAGTTGGAATGGCCAAGAATCCAGTGACAGGCTTGCTTCCAGCCAGCTATGATCAAAAAGATGCCTGGGTCCGAGATAATGTGTACAGTATCCTGGCTGTGTGGGGTTTGGGCCTGG
Note: Users can design additional primers for provided template sequence using Primer3 or NCBI primer-blast.
miRNAs associated with circular RNAs
No of miRNAs
11
Interacting miRNAs (#binding sites)
mmu-miR-9-5p(1), mmu-miR-27b-3p(1), mmu-miR-27a-3p(1), mmu-let-7b-5p(1), mmu-miR-351-5p(1), mmu-miR-199b-3p(1), mmu-miR-199a-3p(1), mmu-miR-98-5p(1), mmu-miR-680(1), mmu-miR-129-5p(1), mmu-miR-484(1)
siRNAs for circular RNA silencing
Junction sequence
TGGAATGGCCAAGAATCCAGTGACAG
siRNA sets
CTGTCACTGGATTCTTGGC, CTGGATTCTTGGCCATTCC, ACTGGATTCTTGGCCATTC
Protein-coding potential of circular RNAs
CPAT analysis
CPAT ORF ID
CPAT Fickett
CPAT Hexamer
Coding probabilty
ORF length
CIRCPHKA1_540_ORF_1
1.1213
0.272442648
0.988668341
906
ORF sequence:
ATGAGGGGACTGCTGCACTGCATGATCAGACAGGTGGATAAAGTAGAGTCCTTCAAGTACAGTCAGAGTACTAAAGATAGCCTCCATGCCAAGTACAACACCAAAACTTGTGCCACTGTGGTGGGTGATGACCAGTGGGGACACCTGCAGTTGGATGCTACTTCTGTGTACCTGCTCTTCCTAGCACAAATGACTGCCTCAGGACTCCATATCATCCACAGCCTAGACGAAGTCAATTTTATACAGAACCTCGTGTTTTACATTGAAGCTGCATATAAAACTGCTGACTTTGGGATATGGGAACGTGGCGATAAGACAAACCAAGGCATCTCGGAATTGAATGCGAGTTCAGTTGGAATGGCCAAGAATCCAGTGACAGGCTTGCTTCCAGCCAGCTATGATCAAAAAGATGCCTGGGTCCGAGATAATGTGTACAGTATCCTGGCTGTGTGGGGTTTGGGCCTGGCATATCGCAAAAATGCTGACCGTGATGAGGACAAGGCAAAGGCCTATGAACTGGAGCAGAGTGTAGTGAAGTTAATGAGGGGACTGCTGCACTGCATGATCAGACAGGTGGATAAAGTAGAGTCCTTCAAGTACAGTCAGAGTACTAAAGATAGCCTCCATGCCAAGTACAACACCAAAACTTGTGCCACTGTGGTGGGTGATGACCAGTGGGGACACCTGCAGTTGGATGCTACTTCTGTGTACCTGCTCTTCCTAGCACAAATGACTGCCTCAGGACTCCATATCATCCACAGCCTAGACGAAGTCAATTTTATACAGAACCTCGTGTTTTACATTGAAGCTGCATATAAAACTGCTGACTTTGGGATATGGGAACGTGGCGATAAGACAAACCAAGGCATCTCGGAATTGAATGCGAGTTCAGTTGGAATGGCCAAG
Peptide sequence:
MRGLLHCMIRQVDKVESFKYSQSTKDSLHAKYNTKTCATVVGDDQWGHLQLDATSVYLLFLAQMTASGLHIIHSLDEVNFIQNLVFYIEAAYKTADFGIWERGDKTNQGISELNASSVGMAKNPVTGLLPASYDQKDAWVRDNVYSILAVWGLGLAYRKNADRDEDKAKAYELEQSVVKLMRGLLHCMIRQVDKVESFKYSQSTKDSLHAKYNTKTCATVVGDDQWGHLQLDATSVYLLFLAQMTASGLHIIHSLDEVNFIQNLVFYIEAAYKTADFGIWERGDKTNQGISELNASSVGMAK
IRESfinder result
IRESfinder score
0.367437754
IRES/non IRES
non-IRES
riboCIRC information
riboCIRC ID
NA
NA
Evidence
Peptide sequence:
NA
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