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mmu_circUsp34_616
Basic information of circular RNA
PanCircBase ID:
mmu_circUsp34_616
mm39_Chr. Position ID:
chr11|23379299|23386079|+
Gene name:
Usp34
Transcript:
ENSMUST00000180046.8
CircRNA type:
Exonic circular (circ)RNA
Exon/Intron count:
6
Exon/intron indexes:
44,45,46,47,48,49
Exon/intron offsets:
0,2946,3178,3319,3880,6607
Genomic length:
6780
Exon/intron sizes in nt:
6,61,47,57,78,95,173
Flanking exon/introns:
chr11:23376795-23379299|chr11:23386079-23388866
Splice length:
616
Other database IDs:
circAtlas: hsa-SCAF8_0001, CIRCpedia: HSA_CIRCpedia_69583
Human Ortholog IDs:
Mature spliced Sequence:
TATTCAGAAGACATGAAGCACAAGACAACTCTTCTGGAACTTCAGAAAATGTTTACATATTTAATGGAGAGTGAGTGCAAAGCCTATAACCCTAGGCCTTTCTGTAAAACTTACACTATGGACAAGCAGCCTCTCAACACTGGGGAGCAGAAAGACATGACAGAGTTCTTTACAGATCTCATTACTAAAGTGGAAGAAATGTCGCCAGAACTGAAAAATACTGTCAAAAGCCTGTTTGGAGGTGTCATTACAAACAATGTTGTTTCGTTGGATTGTGAACATGTTAGTCAAACTGCTGAAGAATTTTATACTGTGAGGTGCCAGGTGGCAGATATGAAGAATATTTATGAGTCTCTGGATGAAGTTACTATTAAAGACACCTTAGAAGGGGACAACATGTACACCTGTTCTCACTGTGGGAAGAAAGTCCGAGCTGAAAAGAGGGCTTGTTTTAAGAAATTACCTCGTATTCTGAGTTTCAATACTATGAGATATACATTTAATATGGTCACGATGATGAAAGAGAAAGTGAATACACACTTTTCTTTCCCTTTACGTTTGGATATGACGCCCTATACAGAAGATTTTCTAATGGGGAAGAGCGACAGGAAAGAAG
Divergent primers for circular RNA PCR
Primer Set-1
Forward primer
Tm
Reverse primer
Tm
Product size
ACGTTTGGATATGACGCCCT
59.46
AGGCTTTGCACTCACTCTCC
59.96
147
Primer Set-2
Forward primer
Tm
Reverse primer
Tm
Product size
ACGTTTGGATATGACGCCCT
59.46
GGCTTTGCACTCACTCTCCA
60.25
146
PCR template sequence:
ATGAAAGAGAAAGTGAATACACACTTTTCTTTCCCTTTACGTTTGGATATGACGCCCTATACAGAAGATTTTCTAATGGGGAAGAGCGACAGGAAAGAAGTATTCAGAAGACATGAAGCACAAGACAACTCTTCTGGAACTTCAGAAAATGTTTACATATTTAATGGAGAGTGAGTGCAAAGCCTATAACCCTAGGCCTT
Note: Users can design additional primers for provided template sequence using Primer3 or NCBI primer-blast.
miRNAs associated with circular RNAs
No of miRNAs
7
Interacting miRNAs (#binding sites)
mmu-miR-27b-3p(1), mmu-miR-27a-3p(1), mmu-miR-199a-5p(1), mmu-miR-30e-5p(1), mmu-miR-30a-5p(1), mmu-miR-128-3p(1), mmu-miR-1904(1)
siRNAs for circular RNA silencing
Junction sequence
GACAGGAAAGAAGTATTCAGAAGACA
siRNA sets
TTCTGAATACTTCTTTCCT, TGAATACTTCTTTCCTGTC, TCTGAATACTTCTTTCCTG
Protein-coding potential of circular RNAs
CPAT analysis
CPAT ORF ID
CPAT Fickett
CPAT Hexamer
Coding probabilty
ORF length
CIRCUSP34_616_ORF_1
0.9411
0.049523729
0.828261151
678
ORF sequence:
ATGAAGCACAAGACAACTCTTCTGGAACTTCAGAAAATGTTTACATATTTAATGGAGAGTGAGTGCAAAGCCTATAACCCTAGGCCTTTCTGTAAAACTTACACTATGGACAAGCAGCCTCTCAACACTGGGGAGCAGAAAGACATGACAGAGTTCTTTACAGATCTCATTACTAAAGTGGAAGAAATGTCGCCAGAACTGAAAAATACTGTCAAAAGCCTGTTTGGAGGTGTCATTACAAACAATGTTGTTTCGTTGGATTGTGAACATGTTAGTCAAACTGCTGAAGAATTTTATACTGTGAGGTGCCAGGTGGCAGATATGAAGAATATTTATGAGTCTCTGGATGAAGTTACTATTAAAGACACCTTAGAAGGGGACAACATGTACACCTGTTCTCACTGTGGGAAGAAAGTCCGAGCTGAAAAGAGGGCTTGTTTTAAGAAATTACCTCGTATTCTGAGTTTCAATACTATGAGATATACATTTAATATGGTCACGATGATGAAAGAGAAAGTGAATACACACTTTTCTTTCCCTTTACGTTTGGATATGACGCCCTATACAGAAGATTTTCTAATGGGGAAGAGCGACAGGAAAGAAGTATTCAGAAGACATGAAGCACAAGACAACTCTTCTGGAACTTCAGAAAATGTTTACATATTTAATGGAGAGTGA
Peptide sequence:
MKHKTTLLELQKMFTYLMESECKAYNPRPFCKTYTMDKQPLNTGEQKDMTEFFTDLITKVEEMSPELKNTVKSLFGGVITNNVVSLDCEHVSQTAEEFYTVRCQVADMKNIYESLDEVTIKDTLEGDNMYTCSHCGKKVRAEKRACFKKLPRILSFNTMRYTFNMVTMMKEKVNTHFSFPLRLDMTPYTEDFLMGKSDRKEVFRRHEAQDNSSGTSENVYIFNGE
IRESfinder result
IRESfinder score
0.714155124
IRES/non IRES
IRES
riboCIRC information
riboCIRC ID
NA
NA
Evidence
Peptide sequence:
NA
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