Basic Information
VIS ID
TVIS20004255
Fusion event
HPV-LINC00111 integration
Validated
Yes
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
HPV16
Reference genome
AY686584
Gene
E2
Start
3020
Integrated sequence
CACCAGGTGGTGCCAACACTGGCTGTATCAAAGAATAAAGCATTACAAGCAATTGAACTGCAACTAACGTTAGAAACAATATATAACTCACAATATAGTA| |ATGAAAAGTGGACATTACAAGACGTTAGCCTTGAAGTGTATTTAACTGCACCAACAGGATGTATAAAAAAACATGGATATACAGTGGAAGTGCAGTTTGA
Host Sequence
Chromosome
chr21
Cytoband
q22.3
Reference genome
GRCh37/hg19
Start
43114241/41694081 (Hg38)
End
43114241/41694081 (Hg38)
Location type
Intronic
Target gene
LINC00111
Nearest miRNA
hsa-let-7c/Upstream/526452; hsa-mir-5692b/Downstream/52691;
Nearest TSS
ENST00000624081/Upstream/14900; ENST00000432830/Downstream/19974;
Nearest CpG islands
None/Target, chr21-CpG: 261/Upstream/4554, chr21-CpG: 81/Downstream/46675
Junction sequence
CCCATCCCTCCACACATCCATCCATCCATTCATCTAT---[GTGAATGGATGTGAG]---TTACTATATTGTGAGTTATATATTGTTTCTAACGTTAGTTGCAGTTCAA
* 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.
Curate