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mmu_circUsp34_543
Basic information of circular RNA
PanCircBase ID:
mmu_circUsp34_543
mm39_Chr. Position ID:
chr11|23343751|23353895|+
Gene name:
Usp34
Transcript:
ENSMUST00000180046.8
CircRNA type:
Exonic circular (circ)RNA
Exon/Intron count:
4
Exon/intron indexes:
29,30,31,32
Exon/intron offsets:
0,7701,9808,10060
Genomic length:
10144
Exon/intron sizes in nt:
210,126,123,84
Flanking exon/introns:
chr11:23342942-23343751|chr11:23353895-23355866
Splice length:
543
Other database IDs:
Human Ortholog IDs:
Mature spliced Sequence:
ATGGTGTTTGTATCTTTGGGTGCACCAAGAAGAGAAAGAAAAGGAGAAGGGGTTCAACTGCCTGCATCTTGCCTCCCACCACCTCAGAAGGACAACATTCCGATGCTTTTGCTGTTACAAGAACCTCATTTAACTACTCTCTTTGATTTATTAGAAATGCTTGCTTCATTTAAACCACCCTCAGGAAAAGTTGCAGTTGATGACAGTGAGAGTTTAAAATGTGAAGAACTTCATCTTCATGCAGAAAATCTTTCAAGGCGTGTCTGGGAGTTGCTGATGCTTCTTCCGACTTGTCCCAACATGCTGACGGCATTCCAGAATGTCTCAGACGAGCAGAGCAATGATGGACTTAATTGGAAGGAACTTCTCAAAATTAAGAGTGCTCATAAGTTGTTATATGCTCTTGAGATTATTGAAGCACTAGGAAAACCTAACAGAAGAATAAGAAGAGAGTCAACGGGAAGTTACAGTGATCTTTATCCAGATTCTGATGATTCAAGTGAAGATCAAGTGGAAAACAGTAAAAATTCCTGGACTTGCAAG
Divergent primers for circular RNA PCR
Primer Set-1
Forward primer
Tm
Reverse primer
Tm
Product size
AGAAGAGAGTCAACGGGAAGT
58.4
CAGGCAGTTGAACCCCTTCT
59.89
163
Primer Set-2
Forward primer
Tm
Reverse primer
Tm
Product size
AGTCAACGGGAAGTTACAGTGA
59.3
CAGGCAGTTGAACCCCTTCT
59.89
156
PCR template sequence:
AAGAAGAGAGTCAACGGGAAGTTACAGTGATCTTTATCCAGATTCTGATGATTCAAGTGAAGATCAAGTGGAAAACAGTAAAAATTCCTGGACTTGCAAGATGGTGTTTGTATCTTTGGGTGCACCAAGAAGAGAAAGAAAAGGAGAAGGGGTTCAACTGCCTGCATCTTGCCTCCCACCACCTCAGAAGGACAACATTC
Note: Users can design additional primers for provided template sequence using Primer3 or NCBI primer-blast.
miRNAs associated with circular RNAs
No of miRNAs
8
Interacting miRNAs (#binding sites)
mmu-miR-31-5p(1), mmu-miR-335-5p(1), mmu-miR-194-5p(1), mmu-miR-705(1), mmu-miR-410-3p(1), mmu-miR-344d-3p(1), mmu-miR-207(1), mmu-miR-1904(1)
siRNAs for circular RNA silencing
Junction sequence
CTGGACTTGCAAGATGGTGTTTGTAT
siRNA sets
ATACAAACACCATCTTGCA, ACACCATCTTGCAAGTCCA, AAACACCATCTTGCAAGTC
Protein-coding potential of circular RNAs
CPAT analysis
CPAT ORF ID
CPAT Fickett
CPAT Hexamer
Coding probabilty
ORF length
CIRCUSP34_543_ORF_1
0.9387
-0.033520067
0.984888002
1086
ORF sequence:
ATGGTGTTTGTATCTTTGGGTGCACCAAGAAGAGAAAGAAAAGGAGAAGGGGTTCAACTGCCTGCATCTTGCCTCCCACCACCTCAGAAGGACAACATTCCGATGCTTTTGCTGTTACAAGAACCTCATTTAACTACTCTCTTTGATTTATTAGAAATGCTTGCTTCATTTAAACCACCCTCAGGAAAAGTTGCAGTTGATGACAGTGAGAGTTTAAAATGTGAAGAACTTCATCTTCATGCAGAAAATCTTTCAAGGCGTGTCTGGGAGTTGCTGATGCTTCTTCCGACTTGTCCCAACATGCTGACGGCATTCCAGAATGTCTCAGACGAGCAGAGCAATGATGGACTTAATTGGAAGGAACTTCTCAAAATTAAGAGTGCTCATAAGTTGTTATATGCTCTTGAGATTATTGAAGCACTAGGAAAACCTAACAGAAGAATAAGAAGAGAGTCAACGGGAAGTTACAGTGATCTTTATCCAGATTCTGATGATTCAAGTGAAGATCAAGTGGAAAACAGTAAAAATTCCTGGACTTGCAAGATGGTGTTTGTATCTTTGGGTGCACCAAGAAGAGAAAGAAAAGGAGAAGGGGTTCAACTGCCTGCATCTTGCCTCCCACCACCTCAGAAGGACAACATTCCGATGCTTTTGCTGTTACAAGAACCTCATTTAACTACTCTCTTTGATTTATTAGAAATGCTTGCTTCATTTAAACCACCCTCAGGAAAAGTTGCAGTTGATGACAGTGAGAGTTTAAAATGTGAAGAACTTCATCTTCATGCAGAAAATCTTTCAAGGCGTGTCTGGGAGTTGCTGATGCTTCTTCCGACTTGTCCCAACATGCTGACGGCATTCCAGAATGTCTCAGACGAGCAGAGCAATGATGGACTTAATTGGAAGGAACTTCTCAAAATTAAGAGTGCTCATAAGTTGTTATATGCTCTTGAGATTATTGAAGCACTAGGAAAACCTAACAGAAGAATAAGAAGAGAGTCAACGGGAAGTTACAGTGATCTTTATCCAGATTCTGATGATTCAAGTGAAGATCAAGTGGAAAACAGTAAAAATTCCTGGACTTGCAAG
Peptide sequence:
MVFVSLGAPRRERKGEGVQLPASCLPPPQKDNIPMLLLLQEPHLTTLFDLLEMLASFKPPSGKVAVDDSESLKCEELHLHAENLSRRVWELLMLLPTCPNMLTAFQNVSDEQSNDGLNWKELLKIKSAHKLLYALEIIEALGKPNRRIRRESTGSYSDLYPDSDDSSEDQVENSKNSWTCKMVFVSLGAPRRERKGEGVQLPASCLPPPQKDNIPMLLLLQEPHLTTLFDLLEMLASFKPPSGKVAVDDSESLKCEELHLHAENLSRRVWELLMLLPTCPNMLTAFQNVSDEQSNDGLNWKELLKIKSAHKLLYALEIIEALGKPNRRIRRESTGSYSDLYPDSDDSSEDQVENSKNSWTCK
IRESfinder result
IRESfinder score
0.801231638
IRES/non IRES
IRES
riboCIRC information
riboCIRC ID
NA
NA
Evidence
Peptide sequence:
NA
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