Basic Information
VIS ID
TVIS20003874
Fusion event
HPV-LINC00596 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
HPV35
Reference genome
Not given
Gene
E1
Start
762
Host Sequence
Chromosome
chr14
Cytoband
q11.2
Reference genome
GRCh37/hg19
Start
24371783/23902574 (Hg38)
End
24371783/23902574 (Hg38)
Location type
Intronic
Target gene
LINC00596
Nearest miRNA
hsa-mir-208a/Upstream/484511; hsa-mir-1185-1/Downstream/240915;
Nearest TSS
ENST00000550708/Upstream/259529; ENST00000543741/Downstream/31994;
Nearest CpG islands
None/Target, chr14-CpG: 35/Upstream/324856, chr14-CpG: 32/Downstream/50987
Nearby gene
LINC00596(+19673) ;
Upstream sequence
AGGTGGGGGTACGTTCTATACGTGCTGATTTAATCGTTTCCGATCTGGGGACATTTGAAGGATGCCAGCAAGGCCCCCTGCTGAAAACTATGCTCCCTAC
Downstream sequence
CTTAGGAGAAAAGAGCCTGATTTCCACAGAGAACAAACATCAGCTGTGCTACAGCCTGCTTTATCCAGCTGAATCTCAGCTTTGTCTGCCGGGATCCCAG
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