Basic Information
VIS ID
TVIS20004436
Fusion event
HPV-FANCC 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
chr9
Cytoband
q22.3
Reference genome
GRCh37.p5
Start
97947013/95184731 (Hg38)
End
97947013/95184731 (Hg38)
Orient
-
Location type
Intron4
Target gene
FANCC
miRNAs that regulate target gene
hsa-mir-26b-5p ; hsa-mir-15b-5p ; hsa-mir-8085 ; hsa-mir-6731-5p ; hsa-mir-5192 ; hsa-mir-6754-5p ; hsa-mir-4441 ; hsa-mir-4270 ; hsa-mir-211-3p ; hsa-mir-3613-3p ; hsa-mir-6760-5p ; hsa-mir-7844-5p ; hsa-mir-5007-5p ; hsa-mir-548x-3p ; hsa-mir-548j-3p ; hsa-mir-548aq-3p ; hsa-mir-548am-3p ; hsa-mir-548aj-3p ; hsa-mir-548ah-3p ; hsa-mir-548ae-3p ; hsa-mir-587 ; hsa-mir-302c-5p ; hsa-mir-873-5p ; hsa-mir-5698 ; hsa-mir-744-3p ; hsa-mir-6848-3p ; hsa-mir-6843-3p ; hsa-mir-4423-5p ; hsa-mir-6501-5p ; hsa-mir-143-5p ; hsa-mir-4430 ; hsa-mir-3652 ; hsa-mir-122-5p ; hsa-mir-504-3p ; hsa-mir-3135b ; hsa-mir-6499-3p ; hsa-mir-1273f ; hsa-mir-367-5p ; hsa-mir-1267 ; hsa-mir-6812-3p ; hsa-mir-6733-3p
Nearest miRNA
hsa-let-7a-1/Upstream/98637; hsa-mir-12126/Downstream/2178823;
Nearest TSS
ENST00000422679/Upstream/34698; ENST00000605700/Downstream/132163;
Nearest CpG islands
None/Target, chr9-CpG: 64/Upstream/98488, chr9-CpG: 25/Downstream/107682
Upstream sequence
AAAAATACATGTGAAAGGTCTGCATAAAGGAAGACCTTGGATCTTAGCAAGAAAAATTCAATGTCACAAAGATGTCAGTTCTCTGGCATAGAAACTCAAT
Downstream sequence
AAGGGAAAGAAGAAAATTATAGAAATAAACAGGCAGCATCATTCTGTTTATATAAAGTTCAAAAGCAGGCACTAAAGGAGATATGGTTCACAGATACACA
Target sequence
GCAGTACCAGTAACAATTCCAAATAGGGTTTTTGGTGGAACTTCAGAAGCTTTTCCAAAATTCACATGGAGAAGCAAGGGGCCAAGAACAGCACATGCT
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.
Curate