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mmu_circUsp34_529
Basic information of circular RNA
PanCircBase ID:
mmu_circUsp34_529
mm39_Chr. Position ID:
chr11|23331224|23335172|+
Gene name:
Usp34
Transcript:
ENSMUST00000180046.8
CircRNA type:
Exonic circular (circ)RNA
Exon/Intron count:
4
Exon/intron indexes:
22,23,24,25
Exon/intron offsets:
0,1329,3176,3788
Genomic length:
3948
Exon/intron sizes in nt:
1,55,11,41,00,160
Flanking exon/introns:
chr11:23327637-23331224|chr11:23335172-23338433
Splice length:
529
Other database IDs:
circAtlas: mmu-Usp34_0035
circAtlas: hsa-USP34_0065
Human Ortholog IDs:
Mature spliced Sequence:
GGTTAAGTTTAGAGCAAGTGGACATTTTATGGCATTGTTTGGTAGAAGACTCTGAGTGCTATGATGATGCACTTCATTGGTTTTTAAATCAAGTTCGAAGTAAAGATCAACATGCAATGGGAATGGAAACCTATAAACATCTTTTCCTGGAGAAGATGCCCCAGCTTAAACCTGAAACAATTAGCATGACTGGCTTAAACCTGTTTCAGCATCTTTGTAACTTGGCTCGATTGGCTACCAGTGCCTATGATGGTGGCTCAAACTCTGAGCTGTGTGGTATGGACCAATTTTGGGGTATTGCATTAAGAGCACAATCAGGTGATGTCAGTAGAGCTGCTATTCAGTATATTAACTCCTACTATATTAATGGTAAAACGGGTTTGGAAAAGGAGCAAGAATTTATTAGTAAGTGCATGGAAAGTCTCATGATAGCTTCTAGCAGTCTTGAACAAGAATCACACTCAAGTCTCACAGTTATAGAACGAGGATTGCTTATGCTGAAGACACATCTGGAAGCATTTAGGAGAAG
Divergent primers for circular RNA PCR
Primer Set-1
Forward primer
Tm
Reverse primer
Tm
Product size
AGCTTCTAGCAGTCTTGAACA
56.96
AGCACTCAGAGTCTTCTACCA
57.84
159
Primer Set-2
Forward primer
Tm
Reverse primer
Tm
Product size
AGCTTCTAGCAGTCTTGAACAAGA
59.96
AGCACTCAGAGTCTTCTACCA
57.84
159
PCR template sequence:
TAGCTTCTAGCAGTCTTGAACAAGAATCACACTCAAGTCTCACAGTTATAGAACGAGGATTGCTTATGCTGAAGACACATCTGGAAGCATTTAGGAGAAGGGTTAAGTTTAGAGCAAGTGGACATTTTATGGCATTGTTTGGTAGAAGACTCTGAGTGCTATGATGATGCACTTCATTGGTTTTTAAATCAAGTTCGAAG
Note: Users can design additional primers for provided template sequence using Primer3 or NCBI primer-blast.
miRNAs associated with circular RNAs
No of miRNAs
1
Interacting miRNAs (#binding sites)
mmu-miR-207(1)
siRNAs for circular RNA silencing
Junction sequence
CATTTAGGAGAAGGGTTAAGTTTAGA
siRNA sets
CTAAACTTAACCCTTCTCC, TAAACTTAACCCTTCTCCT, TCTAAACTTAACCCTTCTC
Protein-coding potential of circular RNAs
CPAT analysis
CPAT ORF ID
CPAT Fickett
CPAT Hexamer
Coding probabilty
ORF length
CIRCUSP34_529_ORF_1
0.6563
-0.06720729
0.279907909
468
ORF sequence:
ATGGGAATGGAAACCTATAAACATCTTTTCCTGGAGAAGATGCCCCAGCTTAAACCTGAAACAATTAGCATGACTGGCTTAAACCTGTTTCAGCATCTTTGTAACTTGGCTCGATTGGCTACCAGTGCCTATGATGGTGGCTCAAACTCTGAGCTGTGTGGTATGGACCAATTTTGGGGTATTGCATTAAGAGCACAATCAGGTGATGTCAGTAGAGCTGCTATTCAGTATATTAACTCCTACTATATTAATGGTAAAACGGGTTTGGAAAAGGAGCAAGAATTTATTAGTAAGTGCATGGAAAGTCTCATGATAGCTTCTAGCAGTCTTGAACAAGAATCACACTCAAGTCTCACAGTTATAGAACGAGGATTGCTTATGCTGAAGACACATCTGGAAGCATTTAGGAGAAGGGTTAAGTTTAGAGCAAGTGGACATTTTATGGCATTGTTTGGTAGAAGACTCTGA
Peptide sequence:
MGMETYKHLFLEKMPQLKPETISMTGLNLFQHLCNLARLATSAYDGGSNSELCGMDQFWGIALRAQSGDVSRAAIQYINSYYINGKTGLEKEQEFISKCMESLMIASSSLEQESHSSLTVIERGLLMLKTHLEAFRRRVKFRASGHFMALFGRRL
IRESfinder result
IRESfinder score
0.665512046
IRES/non IRES
IRES
riboCIRC information
riboCIRC ID
NA
NA
Evidence
Peptide sequence:
NA
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