Basic Information
VIS ID
TVIS20003785
Fusion event
HPV-CDH4 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
3348
End
3397
Orient
+
Integrated sequence
GTGTTTAGCAGCAACGAAGTATCCTCTCCTGAAATTATTAGGCAGCACTT
Host Sequence
Chromosome
chr20
Cytoband
q13.33
Reference genome
GRCh37/hg19
Start
60027384/61452328 (Hg38)
End
60027384/61452328 (Hg38)
Location type
Intronic
Target gene
CDH4
miRNAs that regulate target gene
hsa-mir-1-3p ; hsa-mir-7111-3p ; hsa-mir-5006-3p ; hsa-mir-4755-5p ; hsa-mir-623 ; hsa-mir-1236-3p ; hsa-mir-6515-3p ; hsa-mir-6832-3p ; hsa-mir-211-5p ; hsa-mir-204-5p ; hsa-mir-570-3p
Nearest miRNA
hsa-mir-103a-2/Upstream/887703; hsa-mir-1-1/Downstream/501218;
Nearest TSS
ENST00000382410/Upstream/14781; ENST00000611855/Downstream/117807;
Nearest CpG islands
None/Target, chr20-CpG: 39/Upstream/61594, chr20-CpG: 15/Downstream/92123
Nearest cancer related gene
CDH4(TSG, No orient, 0)
Upstream sequence
TACATGTTGAGTTCCAGGTGTCTTTGGTTTTAATCTCGTGTCAGAAAATTATATGAGATGATGCCTGATGCCTCTTGTCCATAATAGATCTTAGTCCCTCATTTAAGGA
Junction sequence
TACATGTTGAGTTCCAGGTGTCTTTGGTTTTAATCTCGTGTCAGAAAATTATATGAGATGATGCCTGATGCCTCTTGTCCATAATAGATCTTAGTCCCTCATTTAAGGAGGGCCTGTGTTTAGCAGCAACGAAGTATCCTCTCCTGAAACTATTAGGCAGCAC
* 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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