Basic Information
VIS ID
TVIS20003991
Fusion event
HPV-SEM1 integration
Validated
No
Detection method
RNA-Seq
Data source
Curated
Sample type
Tumor
Disease
Head and neck squamous cell carcinoma (HNSCC)
Quality evaluation
Normal
Reported year
2018
PubMed ID
28928286
Virus Sequence
Virus name
HPV
Subtype
HPV33
Reference genome
Not given
Gene
E4
Start
795
Host Sequence
Chromosome
chr7
Cytoband
q21.3
Reference genome
GRCh37/hg19
Start
96251560/96622248 (Hg38)
End
96251560/96622248 (Hg38)
Location type
Exon5
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/402492; hsa-mir-10399/Downstream/1341410;
Nearest TSS
ENST00000635602/Upstream/118725; ENST00000555308/Downstream/23684;
Nearest CpG islands
None/Target, chr7-CpG: 39/Upstream/299924, chr7-CpG: 38/Downstream/87256
Upstream sequence
tatttaattACGTGGGAAAAGGAGACTTGGAGTCAGGAAGGCTTGAGCTGAAAGATTTCCACAGGCTTCAGAGCTCTGGTTTTGAGCACCCTAGACAGAT
Downstream sequence
CAGAACATAAAAGGACATGGAAAAAAAAAATAAAACTAATGTGCTAATCAGTTCAATAAATGCTTGAAGCTGGCCTTAAATCAAATAAAAGACAGGAAAA
Reference
Koneva, L. A., et al. HPV Integration in HNSCC Correlates with Survival Outcomes, Immune Response Signatures, and Candidate Drivers. Mol Cancer Res ,2018,16(1): 90-102.
Curate