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mmu_circPhf20_1018
Basic information of circular RNA
PanCircBase ID:
mmu_circPhf20_1018
mm39_Chr. Position ID:
chr2|156129720|156140636|+
Gene name:
Phf20
Transcript:
ENSMUST00000037401.10
CircRNA type:
Exonic circular (circ)RNA
Exon/Intron count:
6
Exon/intron indexes:
10,11,12,13,14,15
Exon/intron offsets:
0,4665,5613,6296,8848,10720
Genomic length:
10916
Exon/intron sizes in nt:
27,99,91,65,17,91,00,100
Flanking exon/introns:
chr2:156118588-156129720|chr2:156140636-156144702
Splice length:
1018
Other database IDs:
CIRCpedia: MMU_CIRCpedia_221280, circAtlas: mmu-Phf20_0013
circBase: hsa_circ_0115071, circAtlas: hsa-PHF20_0014, CIRCpedia: HSA_CIRCpedia_116640
Human Ortholog IDs:
Mature spliced Sequence:
TTCCAAATACTTTGAAGAAAGTTGATGACTCTGTGACGTTGAATGTGCCAGCTGTGGACCTAGACCACAAGTTTCGATGCAAGGTTCTGGACTGTTTGAAATTTTTCCGCAAGGCTAAATTGCTGCACTATCATATGAAGTATTTCCATGGGATGGAGAAGTCACCAGAGCCAGAGGAGGGCCCAGGGAAGACGCATGTACAGACTCGGGGCTCTGCGGTGCCTGACAAGACAAGCCAGGAGAGCCTAACCAGGAAGCGGGTCTCTGCCAGTTCCCCCACTGCAAAAGAGAAGGAAAAGACTAAAGAGAAGAAATTCAAAGAACTTGTGAGAGTGAAGCCAAAGAAGAAAAAGAAAAAGAAAAAGAAAACCAAGCCTGAATGTCCCTGCAGTGAGGACATCAGTGATACTTCCCAGGAACCTTCTCCACCCAAAACATTTGCTGTCACCAGGTGTGGGTCCTCACACAAGCCTGGGGTCCATATGAGCCCGCAGCTCCATGGTTCAGATAATGGAAACCACAAAGGGAAATTGAAAACCTGTGAGGAGGATAATTTGAGTGAGTCCTCTTCCGAGAGCTTTCTTTGGAGTGATGAGGAATATGGTCAAGATGTTGATGTGACCACCAACCCAGATGAGGAGCTTGAGGGCGACGACCGCTATGATTTTGAGGTGGTCCGCTGCATCTGTGAAGTGCAGGAGGAAAATGACTTCATGATTCAGTGTGAAGAGTGCCAGTGCTGGCAGCACGGGGTCTGCATGGGCTTACTGGAAGAAAACGTGCCTGAGAAATACACCTGCTATGTTTGCCAAGACCCTCCAGGTCAGAGGCCTGGCTTCAAGTACTGGTATGACAAGGAGTGGCTGAGCCGGGGACACATGCATGGTCTGGCATTTCTGGATCAGAACTACTCCCACCAGAATGCCAGGAAGATCGTGGCCACCCACCAGCTGCTCGGGGACGTGCAGAGAGTGATCCAAGTGCTGCACGGCCTGCAGCTCAAGATGAGCATTCTGCA
Divergent primers for circular RNA PCR
Primer Set-1
Forward primer
Tm
Reverse primer
Tm
Product size
GGACGTGCAGAGAGTGATCC
60.18
AGTCCAGAACCTTGCATCGA
59.02
153
Primer Set-2
Forward primer
Tm
Reverse primer
Tm
Product size
GGGACGTGCAGAGAGTGATC
60.18
AGTCCAGAACCTTGCATCGA
59.02
154
PCR template sequence:
AGAATGCCAGGAAGATCGTGGCCACCCACCAGCTGCTCGGGGACGTGCAGAGAGTGATCCAAGTGCTGCACGGCCTGCAGCTCAAGATGAGCATTCTGCATTCCAAATACTTTGAAGAAAGTTGATGACTCTGTGACGTTGAATGTGCCAGCTGTGGACCTAGACCACAAGTTTCGATGCAAGGTTCTGGACTGTTTGAA
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-181a-5p(1), mmu-miR-211-5p(1), mmu-miR-204-5p(1), mmu-miR-322-5p(1), mmu-miR-132-3p(1), mmu-miR-326-3p(1), mmu-miR-149-5p(1), mmu-miR-182-5p(1), mmu-miR-1198-5p(1), mmu-miR-669d-5p(1), mmu-miR-181d-5p(1)
siRNAs for circular RNA silencing
Junction sequence
TGAGCATTCTGCATTCCAAATACTTT
siRNA sets
AAAGTATTTGGAATGCAGA,TATTTGGAATGCAGAATGC,ATTTGGAATGCAGAATGCT
Protein-coding potential of circular RNAs
CPAT analysis
CPAT ORF ID
CPAT Fickett
CPAT Hexamer
Coding probabilty
ORF length
CIRCPHF20_1018_ORF_1
0.9188
0.330971633
0.987013471
909
ORF sequence:
ATGAAGTATTTCCATGGGATGGAGAAGTCACCAGAGCCAGAGGAGGGCCCAGGGAAGACGCATGTACAGACTCGGGGCTCTGCGGTGCCTGACAAGACAAGCCAGGAGAGCCTAACCAGGAAGCGGGTCTCTGCCAGTTCCCCCACTGCAAAAGAGAAGGAAAAGACTAAAGAGAAGAAATTCAAAGAACTTGTGAGAGTGAAGCCAAAGAAGAAAAAGAAAAAGAAAAAGAAAACCAAGCCTGAATGTCCCTGCAGTGAGGACATCAGTGATACTTCCCAGGAACCTTCTCCACCCAAAACATTTGCTGTCACCAGGTGTGGGTCCTCACACAAGCCTGGGGTCCATATGAGCCCGCAGCTCCATGGTTCAGATAATGGAAACCACAAAGGGAAATTGAAAACCTGTGAGGAGGATAATTTGAGTGAGTCCTCTTCCGAGAGCTTTCTTTGGAGTGATGAGGAATATGGTCAAGATGTTGATGTGACCACCAACCCAGATGAGGAGCTTGAGGGCGACGACCGCTATGATTTTGAGGTGGTCCGCTGCATCTGTGAAGTGCAGGAGGAAAATGACTTCATGATTCAGTGTGAAGAGTGCCAGTGCTGGCAGCACGGGGTCTGCATGGGCTTACTGGAAGAAAACGTGCCTGAGAAATACACCTGCTATGTTTGCCAAGACCCTCCAGGTCAGAGGCCTGGCTTCAAGTACTGGTATGACAAGGAGTGGCTGAGCCGGGGACACATGCATGGTCTGGCATTTCTGGATCAGAACTACTCCCACCAGAATGCCAGGAAGATCGTGGCCACCCACCAGCTGCTCGGGGACGTGCAGAGAGTGATCCAAGTGCTGCACGGCCTGCAGCTCAAGATGAGCATTCTGCATTCCAAATACTTTGAAGAAAGTTGA
Peptide sequence:
MKYFHGMEKSPEPEEGPGKTHVQTRGSAVPDKTSQESLTRKRVSASSPTAKEKEKTKEKKFKELVRVKPKKKKKKKKKTKPECPCSEDISDTSQEPSPPKTFAVTRCGSSHKPGVHMSPQLHGSDNGNHKGKLKTCEEDNLSESSSESFLWSDEEYGQDVDVTTNPDEELEGDDRYDFEVVRCICEVQEENDFMIQCEECQCWQHGVCMGLLEENVPEKYTCYVCQDPPGQRPGFKYWYDKEWLSRGHMHGLAFLDQNYSHQNARKIVATHQLLGDVQRVIQVLHGLQLKMSILHSKYFEES
IRESfinder result
IRESfinder score
0.463015817
IRES/non IRES
non-IRES
riboCIRC information
riboCIRC ID
NA
NA
Evidence
Peptide sequence:
NA
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