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mmu_circPhf20_553
Basic information of circular RNA
PanCircBase ID:
mmu_circPhf20_553
mm39_Chr. Position ID:
chr2|156096145|156109462|+
Gene name:
Phf20
Transcript:
ENSMUST00000037401.10
CircRNA type:
Exonic circular (circ)RNA
Exon/Intron count:
3
Exon/intron indexes:
4,5,6
Exon/intron offsets:
0,10055,12929
Genomic length:
13317
Exon/intron sizes in nt:
85,80,388
Flanking exon/introns:
chr2:156093867-156096145|chr2:156109462-156114461
Splice length:
553
Other database IDs:
circAtlas: mmu-Phf20_0018
circBase: hsa_circ_0115065, circAtlas: hsa-SCAF8_0001, CIRCpedia: HSA_CIRCpedia_33986
Human Ortholog IDs:
Mature spliced Sequence:
GAATTTCAAATAAACCAGCAAGTGCTTGCTTGCTGGTCTGACTGTCGATTTTATCCAGCCAGAGTCACTGCTGTGAACAAGGATGGTACTTACACTGTGAAATTTTATGATGGAGTAGTTCAAACTGTCAAACATATTCATGTCAAAGCTTTTTCCAAAGATCAGAATATTGTGGGTAATGCTAGGCCTAAAGAAACAGACCACAAAAGTCTTTCATCGTCTCCTGAGAAACGAGAGAAGTTTAAAGAACAGAGAAAAGTCACGGTCAATGTGAAGAAAGACAAAGTGGAAAAAGCCTTAAAGACAGAAAAGCGGCCCAAGCAACCTGACAAAGAGGGAAAGCTGATCTGCTCAGAAAAAGGCAAAGTGTCAGAGAAAAGCCTTCCTAAGAACGAAAAGGAAGATAAGGAGAACATTTCCGAGAACGAGCGGGAGTACTCCGGGGATGCCCAGGTGGAAAAGAAGCCTGAGAAGGACCTTGTGAAGAACCCACAAGAGAACCTGAAGGAGCCAAAAAGAAAACGAGGCAGACCCCCTTCCATAACTCCTACGG
Divergent primers for circular RNA PCR
Primer Set-1
Forward primer
Tm
Reverse primer
Tm
Product size
GCCTGAGAAGGACCTTGTGA
59.31
GCAGTGACTCTGGCTGGATA
59.17
160
Primer Set-2
Forward primer
Tm
Reverse primer
Tm
Product size
AGCCTGAGAAGGACCTTGTG
59.31
GCAGTGACTCTGGCTGGATA
59.17
161
PCR template sequence:
GTGGAAAAGAAGCCTGAGAAGGACCTTGTGAAGAACCCACAAGAGAACCTGAAGGAGCCAAAAAGAAAACGAGGCAGACCCCCTTCCATAACTCCTACGGGAATTTCAAATAAACCAGCAAGTGCTTGCTTGCTGGTCTGACTGTCGATTTTATCCAGCCAGAGTCACTGCTGTGAACAAGGATGGTACTTACACTGTGA
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-23b-3p(1), mmu-miR-27b-3p(1), mmu-miR-27a-3p(1), mmu-miR-7b-5p(1), mmu-miR-34a-5p(1), mmu-miR-324-5p(1), mmu-miR-23a-3p(1), mmu-miR-29b-1-5p(1), mmu-miR-362-5p(1), mmu-miR-190b-5p(1), mmu-miR-673-5p(1)
siRNAs for circular RNA silencing
Junction sequence
ATAACTCCTACGGGAATTTCAAATAA
siRNA sets
TATTTGAAATTCCCGTAGG, ATTTGAAATTCCCGTAGGA, TTATTTGAAATTCCCGTAG
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
0.492874414
IRES/non IRES
non-IRES
riboCIRC information
riboCIRC ID
NA
NA
Evidence
Peptide sequence:
NA
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