Basic Information
VIS ID
TVIS20003784
Fusion event
HPV-FOXA2 integration
Validated
Yes
Detection method
PCR and Sanger sequencing
Data source
Curated
Sample type
Tumor
Disease
Not given
Quality evaluation
Perfect
Reported year
2015
PubMed ID
25581428
Virus Sequence
Virus name
HPV
Subtype
HPV16
Reference genome
NC_001526.2
Start
3877
End
3929
Orient
-
Integrated sequence
ATTACTGGCGTGCTTTTTGCTTTGCTTTTGTGTGCTTTTGTGTGTCTGCCTAT
Host Sequence
Chromosome
chr20
Cytoband
p11.21
Reference genome
GRCh37/hg19
Start
22535191/22554553 (Hg38)
End
22535191/22554553 (Hg38)
Location type
Intronic
Target gene
FOXA2
miRNAs that regulate target gene
hsa-mir-335-5p ; hsa-mir-1185-2-3p ; hsa-mir-1185-1-3p ; hsa-mir-187-3p ; hsa-mir-124-3p ; hsa-mir-200a-3p ; hsa-mir-199a-3p ; hsa-mir-1290 ; hsa-mir-3167 ; hsa-mir-450a-1-3p ; hsa-mir-5096 ; hsa-mir-6716-5p ; hsa-mir-876-5p
Nearest miRNA
hsa-mir-103a-2/Upstream/4083862; hsa-mir-1-1/Downstream/3653633;
Nearest TSS
ENST00000382410/Upstream/82996; ENST00000635173/Downstream/6371;
Nearest CpG islands
None/Target, chr20-CpG: 39/Upstream/839847, chr20-CpG: 69/Downstream/13776
Nearest cancer related gene
FOXA2(TSG, No orient, 0)
Upstream sequence
CACCATGTAGATGGCACCAGTGCATCCACA
Junction sequence
CACCATGTAGATGGCACCAGTGCATCCACAACATTACTGGCGTGCTTTTTGCTTTGCTTTTGTGTGCTTTTGTGTGTCTGCCTATTAATACGTCCGCTGCTTTTGT
* Color:  Human Sequence / Virus Sequence / Overlapped sequence / Unknown sequence
Reference
Hu, Z., et al. Genome-wide profiling of HPV integration in cervical cancer identifies clustered genomic hot spots and a potential microhomology-mediated integration mechanism. Nat Genet,2015, 47(2): 158-163.
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