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mmu_circUsp9x_356
Basic information of circular RNA
PanCircBase ID:
mmu_circUsp9x_356
mm39_Chr. Position ID:
chrX|13024957|13026142|+
Gene name:
Usp9x
Transcript:
ENSMUST00000089302.11
CircRNA type:
Exonic circular (circ)RNA
Exon/Intron count:
2
Exon/intron indexes:
37,38
Exon/intron offsets:
0,1055
Genomic length:
1185
Exon/intron sizes in nt:
2,26,130
Flanking exon/introns:
chrX:13024031-13024957|chrX:13026142-13026985
Splice length:
356
Other database IDs:
circBase: hsa_circ_0090281
Human Ortholog IDs:
Mature spliced Sequence:
GTATGATGCATTGTGTATTCTCCTGCGTCACAGCAAGAACGTGCGGTTTTGGTTTGCTCACAATGTCCTTTTTAATGTTTCAAATCGATTCTCTGAGTACCTTTTGGAATGCCCTAGTGCAGAAGTGAGAGGTGCATTTGCAAAGCTCATAGTTTTCATTGCACATTTTTCCTTACAAGACGGGCCTTGTCCTTCACCTTTTGCATCTCCTGGACCTTCTAGTCAGGCTTATGACAACTTAAGTTTGAGTGACCACTTACTAAGAGCAGTACTAAATCTCTTGCGGAGGGAGGTTTCAGAGCATGGACGTCATTTACAGCAGTATTTCAACTTGTTCGTAATGTATGCCAATTTAG
Divergent primers for circular RNA PCR
Primer Set-1
Forward primer
Tm
Reverse primer
Tm
Product size
CTCTTGCGGAGGGAGGTTTC
60.39
GTGAGCAAACCAAAACCGCA
60.18
140
Primer Set-2
Forward primer
Tm
Reverse primer
Tm
Product size
CTCTTGCGGAGGGAGGTTTC
60.39
TGTGAGCAAACCAAAACCGC
60.18
141
PCR template sequence:
TTACTAAGAGCAGTACTAAATCTCTTGCGGAGGGAGGTTTCAGAGCATGGACGTCATTTACAGCAGTATTTCAACTTGTTCGTAATGTATGCCAATTTAGGTATGATGCATTGTGTATTCTCCTGCGTCACAGCAAGAACGTGCGGTTTTGGTTTGCTCACAATGTCCTTTTTAATGTTTCAAATCGATTCTCTGAGTAC
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-429-3p(1), mmu-miR-200b-3p(1), mmu-miR-200c-3p(1), mmu-miR-494-3p(1), mmu-miR-7a-2-3p(1)
siRNAs for circular RNA silencing
Junction sequence
TATGCCAATTTAGGTATGATGCATTG
siRNA sets
NA
Protein-coding potential of circular RNAs
CPAT analysis
CPAT ORF ID
CPAT Fickett
CPAT Hexamer
Coding probabilty
ORF length
CIRCUSP9X_356_ORF_1
0.6786
-0.197063714
0.022656916
144
ORF sequence:
ATGTATGCCAATTTAGGTATGATGCATTGTGTATTCTCCTGCGTCACAGCAAGAACGTGCGGTTTTGGTTTGCTCACAATGTCCTTTTTAATGTTTCAAATCGATTCTCTGAGTACCTTTTGGAATGCCCTAGTGCAGAAGTGA
Peptide sequence:
MYANLGMMHCVFSCVTARTCGFGLLTMSFLMFQIDSLSTFWNALVQK
IRESfinder result
IRESfinder score
0.731786143
IRES/non IRES
IRES
riboCIRC information
riboCIRC ID
NA
NA
Evidence
Peptide sequence:
NA
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