Basic Information
VIS ID
TVIS20003701
Fusion event
HPV-TBC1D4 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
4467
End
4358
Orient
-
Integrated sequence
GCTGAACAAATATTACAATATGGAAGTATGGGTGTATTTTTTGGTGGGTTAGGAATTGGAACAGGGTCGGGTACAGGCGGACGCACTGGGTATATTCCATTGGGAACAAG
Host Sequence
Chromosome
chr13
Cytoband
q22.2
Reference genome
GRCh37/hg19
Start
75739661/75165524 (Hg38)
End
75739661/75165524 (Hg38)
Location type
Intronic
Fragile sites / regions
FRA13E
Target gene
TBC1D4
miRNAs that regulate target gene
hsa-mir-98-5p ; hsa-mir-30a-5p ; hsa-mir-19b-3p ; hsa-mir-29b-2-5p ; hsa-mir-7150 ; hsa-mir-4736 ; hsa-mir-4763-3p ; hsa-mir-1207-5p ; hsa-mir-1193 ; hsa-mir-6722-3p ; hsa-mir-1909-3p ; hsa-mir-8069 ; hsa-mir-4456 ; hsa-mir-4494 ; hsa-mir-4463
Nearest miRNA
hsa-mir-1297/Upstream/8947200; hsa-mir-1267/Downstream/2532488;
Nearest TSS
ENST00000623511/Upstream/608988; ENST00000434832/Downstream/84956;
Nearest CpG islands
None/Target, chr13-CpG: 551/Upstream/1029843, chr13-CpG: 197/Downstream/315192
Upstream sequence
AGGAGAGCGCTGAGGTTAAATGAGATCGTATGGG
Junction sequence
AGGAGAGCGCTGAGGTTAAATGAGATCGTATGGGAAAGAGTGTTTGTTCCCAATGGAATATACCCAGTGCGTCGGCCTGTACCCGACCCTGTTCCAATTCCTAACCCACCAAAAAATACACCCATACTTCCATATTGTAATATTTGATCAGCA
* 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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