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mmu_circUsp34_550
Basic information of circular RNA
PanCircBase ID:
mmu_circUsp34_550
mm39_Chr. Position ID:
chr11|23382245|23386079|+
Gene name:
Usp34
Transcript:
ENSMUST00000180046.8
CircRNA type:
Exonic circular (circ)RNA
Exon/Intron count:
5
Exon/intron indexes:
45,46,47,48,49
Exon/intron offsets:
0,232,373,934,3661
Genomic length:
3834
Exon/intron sizes in nt:
147,57,78,95,173
Flanking exon/introns:
chr11:23379365-23382245|chr11:23386079-23388866
Splice length:
550
Other database IDs:
CIRCpedia: MMU_CIRCpedia_13858, circAtlas: mmu-Usp34_0055
circAtlas: hsa-USP34_0092, CIRCpedia: HSA_CIRCpedia_92033
Human Ortholog IDs:
Mature spliced Sequence:
GAGAGTGAGTGCAAAGCCTATAACCCTAGGCCTTTCTGTAAAACTTACACTATGGACAAGCAGCCTCTCAACACTGGGGAGCAGAAAGACATGACAGAGTTCTTTACAGATCTCATTACTAAAGTGGAAGAAATGTCGCCAGAACTGAAAAATACTGTCAAAAGCCTGTTTGGAGGTGTCATTACAAACAATGTTGTTTCGTTGGATTGTGAACATGTTAGTCAAACTGCTGAAGAATTTTATACTGTGAGGTGCCAGGTGGCAGATATGAAGAATATTTATGAGTCTCTGGATGAAGTTACTATTAAAGACACCTTAGAAGGGGACAACATGTACACCTGTTCTCACTGTGGGAAGAAAGTCCGAGCTGAAAAGAGGGCTTGTTTTAAGAAATTACCTCGTATTCTGAGTTTCAATACTATGAGATATACATTTAATATGGTCACGATGATGAAAGAGAAAGTGAATACACACTTTTCTTTCCCTTTACGTTTGGATATGACGCCCTATACAGAAGATTTTCTAATGGGGAAGAGCGACAGGAAAGAAG
Divergent primers for circular RNA PCR
Primer Set-1
Forward primer
Tm
Reverse primer
Tm
Product size
ACGTTTGGATATGACGCCCT
59.46
CTGCTCCCCAGTGTTGAGAG
60.04
146
Primer Set-2
Forward primer
Tm
Reverse primer
Tm
Product size
ACGTTTGGATATGACGCCCT
59.46
TTCTGCTCCCCAGTGTTGAG
59.6
148
PCR template sequence:
ATGAAAGAGAAAGTGAATACACACTTTTCTTTCCCTTTACGTTTGGATATGACGCCCTATACAGAAGATTTTCTAATGGGGAAGAGCGACAGGAAAGAAGGAGAGTGAGTGCAAAGCCTATAACCCTAGGCCTTTCTGTAAAACTTACACTATGGACAAGCAGCCTCTCAACACTGGGGAGCAGAAAGACATGACAGAGT
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-27b-3p(1), mmu-miR-27a-3p(1), mmu-miR-199a-5p(1), mmu-miR-128-3p(1), mmu-miR-1904(1)
siRNAs for circular RNA silencing
Junction sequence
GACAGGAAAGAAGGAGAGTGAGTGCA
siRNA sets
ACTCTCCTTCTTTCCTGTC, TCACTCTCCTTCTTTCCTG, CTCACTCTCCTTCTTTCCT
Protein-coding potential of circular RNAs
CPAT analysis
CPAT ORF ID
CPAT Fickett
CPAT Hexamer
Coding probabilty
ORF length
CIRCUSP34_550_ORF_1
1.1758
0.093478919
0.722848571
507
ORF sequence:
ATGGACAAGCAGCCTCTCAACACTGGGGAGCAGAAAGACATGACAGAGTTCTTTACAGATCTCATTACTAAAGTGGAAGAAATGTCGCCAGAACTGAAAAATACTGTCAAAAGCCTGTTTGGAGGTGTCATTACAAACAATGTTGTTTCGTTGGATTGTGAACATGTTAGTCAAACTGCTGAAGAATTTTATACTGTGAGGTGCCAGGTGGCAGATATGAAGAATATTTATGAGTCTCTGGATGAAGTTACTATTAAAGACACCTTAGAAGGGGACAACATGTACACCTGTTCTCACTGTGGGAAGAAAGTCCGAGCTGAAAAGAGGGCTTGTTTTAAGAAATTACCTCGTATTCTGAGTTTCAATACTATGAGATATACATTTAATATGGTCACGATGATGAAAGAGAAAGTGAATACACACTTTTCTTTCCCTTTACGTTTGGATATGACGCCCTATACAGAAGATTTTCTAATGGGGAAGAGCGACAGGAAAGAAGGAGAGTGA
Peptide sequence:
MDKQPLNTGEQKDMTEFFTDLITKVEEMSPELKNTVKSLFGGVITNNVVSLDCEHVSQTAEEFYTVRCQVADMKNIYESLDEVTIKDTLEGDNMYTCSHCGKKVRAEKRACFKKLPRILSFNTMRYTFNMVTMMKEKVNTHFSFPLRLDMTPYTEDFLMGKSDRKEGE
IRESfinder result
IRESfinder score
0.674812436
IRES/non IRES
IRES
riboCIRC information
riboCIRC ID
NA
NA
Evidence
Peptide sequence:
NA
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