Basic Information
VIS ID
TVIS20004399
Fusion event
HPV-BABAM2 integration
Validated
Yes
Detection method
DIPS-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
Gene
E1
Start
2383
Integrated sequence
TACTATATGGTGCAGCTAACACAGGTAAATCATTATTTGGTATGAGTTTAATGAAATTTCTGCAAGGGTCTGTAATATGTTTTGTAAATTCTAAAAGCCA| |TTTTTGGTTACAACCATTAGCAGATGCCAAAATAGGTATGTTAGATGATGCTACAGTGCCCTGTTGGAACTACATAGATGACAATTTAAGAAATGCATTG
Host Sequence
Chromosome
chr2
Cytoband
p23.2
Reference genome
GRCh37.p5
Start
28508231/28285364 (Hg38)
End
28508231/28285364 (Hg38)
Orient
-
Location type
Intron11
Target gene
BABAM2
miRNAs that regulate target gene
hsa-mir-124-3p
Nearest miRNA
hsa-mir-1301/Upstream/288915; hsa-mir-10b/Downstream/4246789;
Nearest TSS
ENST00000437798/Upstream/390744; ENST00000460736/Downstream/25095;
Nearest CpG islands
None/Target, chr2-CpG: 135/Upstream/394467, chr2-CpG: 302/Downstream/104733
Upstream sequence
GTATGGCGTGCTTTACCTGCTTCATTTCCAACCCTGAGCTTAAAGTTTTTTCCAGTCTTGGGAATGGGAAAAGAGGAGCACAGAGGTCAGTTCACCTGCC
Downstream sequence
TTTTTAACATTTCTGGGGAAAATATCCCCATTCCACACATTCTAGTGGGTCAGACATTGTCCTATAATTGTAATATCCCTGCACGGTATAAGTCCAGCAT
Target sequence
AAAGCTTGCCCACCTCGAGTACACATGCCTTCCTCACTCAACACTCGGCTTCACCCAGATAAGCTGTTCCCCACCCATCTTGCAGACTGAGTGGCTGAT
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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