Basic Information
VIS ID
TVIS20004440
Fusion event
HPV-CCSER1 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
chr4
Cytoband
q22.1
Reference genome
GRCh37.p5
Start
92436058/91514907 (Hg38)
End
92436058/91514907 (Hg38)
Orient
+
Location type
Intron9
Fragile sites / regions
FRA4E
Target gene
CCSER1
miRNAs that regulate target gene
hsa-mir-544a
Nearest miRNA
hsa-mir-12113/Upstream/4214324; hsa-mir-1243/Downstream/7482480;
Nearest TSS
ENST00000502981/Upstream/189601; ENST00000505511/Downstream/372979;
Nearest CpG islands
None/Target, chr4-CpG: 46/Upstream/675791, chr4-CpG: 26/Downstream/667559
Upstream sequence
GGCACCATGGAGCACCAATGGTTTAGTTCCAGTCAAAGTCTGAAAACCTGAGAACCATGAGAGCTGATGGCATAGTTCCAGTCTGAAAGACAGCAGGCTC
Downstream sequence
AGGTTTTCAACTTAATAGTTGGATGATGCCTGCCTACATTAGGAAGAACAAACTGCTTAACTTATTCTACTGATTTACAGGTTAAGCTTATCAAAAAACA
Target sequence
ACAATACAGGACGACAAAGTCTCTCAGTTAAAAGGCAATTAAGCAGGAAGAATTCTCTTTTAAGCAGAGGAGAAATATCCTTTTTATTTTTTGTTTTTC
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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