Basic Information
VIS ID
TVIS20003985
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
E7
Start
853
Host Sequence
Chromosome
chr7
Cytoband
q21.3
Reference genome
GRCh37/hg19
Start
96285521/96656209 (Hg38)
End
96285521/96656209 (Hg38)
Location type
Exon2
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/436453; hsa-mir-10399/Downstream/1307449;
Nearest TSS
ENST00000635602/Upstream/10277; ENST00000555308/Downstream/8036;
Nearest CpG islands
None/Target, chr7-CpG: 39/Upstream/333885, chr7-CpG: 38/Downstream/53295
Upstream sequence
ACTGGTACACCAAAAGAAATCTTACATATTTTTATTCTTTTACAAGTGGCATTAATAAAGAATAACTTAACATGAAATATATAGGATCAAAATGAAGAAA
Downstream sequence
CCTGATCTCTCTGGTGTCCGTTTCTGGCTTTTGGTTGGCCAAACCCACAAGTCTCCAAATTCTTAGTTGGAGTCCTCATGCCTACTGCCTGACCATTCTC
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