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mmu_circUsp48_410
Basic information of circular RNA
PanCircBase ID:
mmu_circUsp48_410
mm39_Chr. Position ID:
chr4|137333062|137335493|+
Gene name:
Usp48
Transcript:
ENSMUST00000105840.8
CircRNA type:
Exonic circular (circ)RNA
Exon/Intron count:
3
Exon/intron indexes:
3,4,5
Exon/intron offsets:
0,937,2306
Genomic length:
2431
Exon/intron sizes in nt:
15,71,28,125
Flanking exon/introns:
chr4:137331954-137333062|chr4:137335493-137336308
Splice length:
410
Other database IDs:
circAtlas: mmu-Usp48_0056
CIRCpedia: HSA_CIRCpedia_30127
Human Ortholog IDs:
Mature spliced Sequence:
AATTCCTTTGTGGGCTTGACTAACCTGGGAGCCACCTGCTACGTCAACACCTTTCTCCAGGTGTGGTTCCTCAACTTGGAGCTTCGGCAGGCGCTGTACTTATGCCCCAGCACCTGCAGTGATTACACGAAGGGAGATGGGATCCATGGGGGAAAAGATTATGAGCCTCAGACAATTTGTGAGCATCTTCAGTACTTGTTTGCTTTGTTGCAAAACAGTAACAGACGATACATCGATCCTTCAGGATTTGTTAAAGCCTTGGGCTTAGATACTGGGCAGCAGCAGGATGCACAAGAGTTTTCCAAGCTCTTTATGTCGCTGTTGGAAGACACTTTGTCTAAACAGAAGAACCCGGATGTTCGGAATGTTGTGCAGCAGCAGTTCTGTGGAGAATATGCCTATGTGACTGT
Divergent primers for circular RNA PCR
Primer Set-1
Forward primer
Tm
Reverse primer
Tm
Product size
TGTCGCTGTTGGAAGACACT
59.54
AGGTGTTGACGTAGCAGGTG
59.97
149
Primer Set-2
Forward primer
Tm
Reverse primer
Tm
Product size
TGTCGCTGTTGGAAGACACT
59.54
TGAGGAACCACACCTGGAGA
60.11
170
PCR template sequence:
TTATGTCGCTGTTGGAAGACACTTTGTCTAAACAGAAGAACCCGGATGTTCGGAATGTTGTGCAGCAGCAGTTCTGTGGAGAATATGCCTATGTGACTGTAATTCCTTTGTGGGCTTGACTAACCTGGGAGCCACCTGCTACGTCAACACCTTTCTCCAGGTGTGGTTCCTCAACTTGGAGCTTCGGCAGGCGCTGTACT
Note: Users can design additional primers for provided template sequence using Primer3 or NCBI primer-blast.
miRNAs associated with circular RNAs
No of miRNAs
2
Interacting miRNAs (#binding sites)
mmu-miR-7b-5p(1), mmu-miR-3065-5p(1)
siRNAs for circular RNA silencing
Junction sequence
CCTATGTGACTGTAATTCCTTTGTGG
siRNA sets
ACAAAGGAATTACAGTCAC, AAAGGAATTACAGTCACAT, CAAAGGAATTACAGTCACA
Protein-coding potential of circular RNAs
CPAT analysis
CPAT ORF ID
CPAT Fickett
CPAT Hexamer
Coding probabilty
ORF length
CIRCUSP48_410_ORF_5
0.9562
0.176383483
0.128014141
117
ORF sequence:
ATGTCGCTGTTGGAAGACACTTTGTCTAAACAGAAGAACCCGGATGTTCGGAATGTTGTGCAGCAGCAGTTCTGTGGAGAATATGCCTATGTGACTGTAATTCCTTTGTGGGCTTGA
Peptide sequence:
MSLLEDTLSKQKNPDVRNVVQQQFCGEYAYVTVIPLWA
IRESfinder result
IRESfinder score
0.542286649
IRES/non IRES
IRES
riboCIRC information
riboCIRC ID
NA
NA
Evidence
Peptide sequence:
NA
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