Basic Information
VIS ID
TVIS20003686
Fusion event
HPV-FHIT 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
2812
End
2742
Orient
-
Integrated sequence
ACAAGGAAAACGATGGAGACTCTTTGCCAACGTTTAAATGTGTGTCAGGACAAAATACTAACACATTATGA
Host Sequence
Chromosome
chr3
Cytoband
p14.2
Reference genome
GRCh37/hg19
Start
60580409/60594676 (Hg38)
End
60580409/60594676 (Hg38)
Location type
Intronic
Fragile sites / regions
FRA3B
Target gene
FHIT
miRNAs that regulate target gene
hsa-mir-143-3p ; hsa-mir-217 ; hsa-mir-331-3p ; hsa-mir-625-5p
Nearest miRNA
hsa-let-7g/Upstream/4742082; hsa-mir-12124/Downstream/23129;
Nearest TSS
ENST00000440867/Upstream/513836; ENST00000475527/Downstream/656708;
Nearest CpG islands
None/Target, chr3-CpG: 148/Upstream/1544458, chr3-CpG: 48/Downstream/656256
Nearest cancer related gene
FHIT(TSG, No orient, 0)
Upstream sequence
TTTCTCGCTCCATCTCTAGCACTATCTGTGTCTGGGGTTTATTTATTTTATGCCATTCCCAAGTGTTGCCCCCTGAACATCTGACCACCCAGCGCAAGGTGACTCTGATCACTTGAGACATCGGGTTTCTAGGTTAGCCACCTCCATCTTCCTGTGCCAACTCCCTCATGTCAGGTTACACCTGATTCCTCCTCCTCGCTTCCCTCTCCTCTCCCCTTCCAACACTATAAAGGGTTTTCCATTCCCCTACTTCCT
Junction sequence
TTTCTCGCTCCATCTCTAGCACTATCTGTGTCTGGGGTTTATTTATTTTATGCCATTCCCAAGTGTTGCCCCCTGAACATCTGACCACCCAGCGCAAGGTGACTCTGATCACTTGAGACATCGGGTTTCTAGGTTAGCCACCTCCATCTTCCTGTGCCAACTCCCTCATGTCAGGTTACACCTGATTCCTCCTCCTCGCTTCCCTCTCCTCTCCCCTTCCAACACTATAAAGGGTTTTCCATTCCCCTACTTCCT
* 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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