Basic Information
VIS ID
TVIS20004428
Fusion event
HPV-TRAF3 integration
Validated
Yes
Detection method
APOT-PCR
Data source
Curated
Sample type
Tumor
Disease
Oropharyngeal squamous cell carcinoma (OSCC)
Quality evaluation
Normal
Reported year
2014
PubMed ID
24586376
Virus Sequence
Virus name
HPV
Subtype
HPV16
Reference genome
NC_001526.1
Host Sequence
Chromosome
chr14
Cytoband
q32.32
Reference genome
GRCh37.p5
Start
103336522/102870185 (Hg38)
End
103336522/102870185 (Hg38)
Orient
+
Location type
Exon3
Target gene
TRAF3
miRNAs that regulate target gene
hsa-mir-32-5p ; hsa-mir-26b-5p ; hsa-mir-3191-3p ; hsa-mir-8085 ; hsa-mir-6731-5p ; hsa-mir-4707-3p ; hsa-mir-6746-5p ; hsa-mir-574-5p ; hsa-mir-4455 ; hsa-mir-129-5p ; hsa-mir-6867-5p ; hsa-mir-4694-5p ; hsa-mir-4286 ; hsa-mir-662 ; hsa-mir-3178 ; hsa-mir-34a-5p ; hsa-mir-361-3p ; hsa-mir-3679-3p ; hsa-mir-4639-3p ; hsa-mir-548e-5p ; hsa-mir-6777-3p ; hsa-mir-6805-5p ; hsa-mir-6846-5p ; hsa-mir-6848-5p
Nearest miRNA
hsa-mir-1185-1/Upstream/330459; hsa-mir-12121/Downstream/1247220;
Nearest TSS
ENST00000550708/Upstream/39831; ENST00000558880/Downstream/1742;
Nearest CpG islands
None/Target, chr14-CpG: 35/Upstream/91817, chr14-CpG: 27/Downstream/37315
Upstream sequence
TATGTGTTTGGGTAAAATAGAAAGGATGGAAGCATATTTGATCATGTTTTGTTCCCAACACATATTAAAGTTGGGAAGGATTCTTGTGTTGCCTAAAACT
Downstream sequence
ACTCCTCTTTCCTAAAATGGAGTCGAGTAAAAAGATGGACTCTCCTGGCGCGCTGCAGACTAACCCGCCGCTAAAGCTGCACACTGACCGCAGTGCTGGG
Target sequence
GAAAGACAGCAGGTCTCAGGCACTTTTGCTTTCCCAAAGCTGTGTTTGTTTCCTTGCATGAGAGGATATGATGGCACTCTACTGTTTTTTCCCGACAGA
Reference
Olthof, N. C., et al.Comprehensive analysis of HPV16 integration in OSCC reveals no significant impact of physical status on viral oncogene and virally disrupted human gene expression.2014, PLoS One 9(2): e88718.
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