Basic Information
VIS ID
TVIS20004426
Fusion event
HPV-SMA4 integration
Validated
Yes
Detection method
APOT-PCR
Data source
Curated
Sample type
Tumor
Disease
Oropharyngeal squamous cell carcinoma (OSCC)
Quality evaluation
Normal
Reported year
2014
PubMed ID
24586376
Virus Sequence
Virus name
HPV
Subtype
HPV16
Reference genome
NC_001526.1
Host Sequence
Chromosome
chr5
Cytoband
q13
Reference genome
GRCh37.p5
Start
69451328/70155501 (Hg38)
End
69451328/70155501 (Hg38)
Orient
+
Location type
Intron14
Target gene
SMA4
Nearest miRNA
hsa-mir-10397/Upstream/10451798; hsa-mir-103a-1/Downstream/2013966;
Nearest TSS
ENST00000502646/Upstream/84837; ENST00000602697/Downstream/294135;
Nearest CpG islands
None/Target, chr5-CpG: 87/Upstream/105507, chr5-CpG: 39/Downstream/259628
Upstream sequence
TCAGAATTTAGTCCTCAACTCAAATATTTTATTCATTCAAACGCTTATTCAAACTACCGAATCCTCCAATAACAGAAAGTATAGTGTCCATCCTGAAGAC
Downstream sequence
TCACAGAAAGAAAGAATACAGGAAGACAAGATGCGAAAGTTATGTCAGTGGCTTTCATTCATCACACCACTACGTACTGGTTCTCTAGTACTGTGCTGTT
Target sequence
TTTCATCCCATCTCACAGCATGTTTTCTCCTAGTACACCCTGATTGTCCAAGGACTTCTGAGAACACCATTCCAGAAGAGGTCATGATCTCAACAACTG
Reference
Olthof, N. C., et al.Comprehensive analysis of HPV16 integration in OSCC reveals no significant impact of physical status on viral oncogene and virally disrupted human gene expression.2014, PLoS One 9(2): e88718.
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