Basic Information
VIS ID
TVIS20005048
Fusion event
HPV-SEM1 integration
Validated
No
Detection method
WGS, RNA-seq, Whole-Exome sequencing, PCR
Data source
Curated
Sample type
Tumor
Disease
Head and neck squamous cell carcinoma (HNSCC)
Quality evaluation
Perfect
Reported year
2014
PubMed ID
25313082
Virus Sequence
Virus name
HPV
Subtype
HPV33
Reference genome
Not given
Gene
E2
Start
2999
Host Sequence
Chromosome
chr7
Cytoband
q21.3
Reference genome
GRCh37/hg19
Start
96291800/96662488 (Hg38)
End
96291800/96662488 (Hg38)
Location type
Intronic
Target gene
SEM1
miRNAs that regulate target gene
hsa-mir-26b-5p ; hsa-mir-30c-5p ; hsa-mir-599 ; hsa-mir-653-5p ; hsa-mir-3161 ; hsa-mir-6807-5p ; hsa-mir-526b-5p ; hsa-mir-1233-3p ; hsa-mir-1225-3p ; hsa-mir-5590-3p ; hsa-mir-142-5p ; hsa-mir-8054 ; hsa-mir-548l ; hsa-mir-548k ; hsa-mir-548av-5p ; hsa-mir-559 ; hsa-mir-548y ; hsa-mir-548w ; hsa-mir-548o-5p ; hsa-mir-548j-5p ; hsa-mir-548i ; hsa-mir-548h-5p ; hsa-mir-548d-5p ; hsa-mir-548c-5p ; hsa-mir-548bb-5p ; hsa-mir-548b-5p ; hsa-mir-548ay-5p ; hsa-mir-548au-5p ; hsa-mir-548as-5p ; hsa-mir-548ar-5p ; hsa-mir-548aq-5p ; hsa-mir-548ap-5p ; hsa-mir-548am-5p ; hsa-mir-548ak ; hsa-mir-548ae-5p ; hsa-mir-548ad-5p ; hsa-mir-548ab ; hsa-mir-548a-5p
Nearest miRNA
hsa-mir-10525/Upstream/442732; hsa-mir-10399/Downstream/1301170;
Nearest TSS
ENST00000635602/Upstream/16556; ENST00000555308/Downstream/1757;
Nearest CpG islands
None/Target, chr7-CpG: 39/Upstream/340164, chr7-CpG: 38/Downstream/47016
Junction sequence
TGAGAACACATGGACACATG---[TGTTA]---TTACTTAATGTCTCTAATGCCATTTG
* Color:  Human Sequence / Virus Sequence / Overlapped sequence / Unknown sequence
Reference
Parfenov, M., et al. Characterization of HPV and host genome interactions in primary head and neck cancers. Proc Natl Acad Sci U S A,2014,111(43): 15544-15549.
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