Basic Information
VIS ID
TVIS20002783
Fusion event
HPV-SMARCA4 integration
Validated
No
Detection method
HIVID
Data source
Curated
Sample type
Tumor
Disease
Squamous-cell carcinoma (SCC)
Quality evaluation
Normal
Reported year
2015
PubMed ID
25581428
Virus Sequence
Virus name
HPV
Subtype
HPV16
Reference genome
NC_001526.2
Host Sequence
Chromosome
chr19
Cytoband
p13.2
Reference genome
GRCh37/hg19
Start
11072671/10961995 (Hg38)
End
11072671/10961995 (Hg38)
Location type
Intronic
Fragile sites / regions
FRA19B
Target gene
SMARCA4
miRNAs that regulate target gene
hsa-mir-21-5p ; hsa-mir-155-5p ; hsa-mir-34a-5p ; hsa-mir-98-5p ; hsa-let-7b-5p ; hsa-mir-342-5p ; hsa-mir-615-3p ; hsa-mir-222-3p ; hsa-mir-16-5p ; hsa-mir-139-5p
Nearest miRNA
hsa-mir-1181/Upstream/132960; hsa-let-7e/Downstream/151479;
Nearest TSS
ENST00000633603/Upstream/674; ENST00000647011/Downstream/22157;
Nearest CpG islands
None/Target, chr19-CpG: 112/Upstream/331, chr19-CpG: 22/Downstream/25724
Nearest cancer related gene
SMARCA4(TSG, No orient, 0)
Upstream sequence
aattgggaggatcacttgggcccaggaggtcaggctgcagtgaaccatcatcacgcctctgtactccagcctaggtgacagagtgtgaccctgtctcaaa
Downstream sequence
CAGTGACTCCTTGGGGAAAGTAGCAAGGGAATAAGCGGAAAAGCCGCTTCGCAGGAATTTGAAGCAAGTTTTCAGtttggattgataggctgcattcaag
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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