Basic Information
VIS ID
TVIS20003881
Fusion event
HPV-LSMEM2 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
HPV16
Reference genome
Not given
Gene
E1
Start
666
Host Sequence
Chromosome
chr3
Cytoband
p21.31
Reference genome
GRCh37/hg19
Start
50318864/50281433 (Hg38)
End
50318864/50281433 (Hg38)
Location type
Intron1
Target gene
LSMEM2
miRNAs that regulate target gene
hsa-mir-335-5p ; hsa-mir-124-3p
Nearest miRNA
hsa-mir-12127/Upstream/8136; hsa-let-7g/Downstream/393647;
Nearest TSS
ENST00000440867/Upstream/2406; ENST00000629828/Downstream/7206;
Nearest CpG islands
None/Target, chr3-CpG: 148/Upstream/4445, chr3-CpG: 67/Downstream/10535
Upstream sequence
CTGCAAGCAAGTTGCTGCCTGTGACCACAGTCTGCAGAGGCCAGAGAGAGCAGGAAAGGAAATGGAAAGGAACCTCACCTTCATGCTTGGGGAAAAGGAG
Downstream sequence
ctcactgcaacctctgcctcccaggttcaagtgattctcctgtctcagcctcccaagtagctgggactacaggcgcctgccaccatacctggctaatttt
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