Basic Information
VIS ID
TVIS20003807
Fusion event
HPV-CGREF1 integration
Validated
Yes
Detection method
PCR and Sanger sequencing
Data source
Curated
Sample type
Cell line
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
4941
End
4990
Orient
-
Integrated sequence
AAGTTGTAGACCCTGCTTTTGTAACCACTCCCACTAAACTTATTACATAT
Host Sequence
Chromosome
chr2
Cytoband
p23.3
Reference genome
GRCh37/hg19
Start
27318113/27095245 (Hg38)
End
27318113/27095245 (Hg38)
Location type
Intronic
Target gene
CGREF1
Nearest miRNA
hsa-mir-1301/Upstream/1766524; hsa-mir-10b/Downstream/901122;
Nearest TSS
ENST00000437798/Upstream/580; ENST00000622011/Downstream/6905;
Nearest CpG islands
None/Target, chr2-CpG: 135/Upstream/8343, chr2-CpG: 78/Downstream/23454
Upstream sequence
ATCTCCCACCCTTCTGTCCTGAGAACAGTTTCCCCGCACCCACAGCCAA
Junction sequence
ATCTCCCACCCTTCTGTCCTGAGAACAGTTTCCCCGCACCCACAGCCAAATAAAGTTGTAGACCCTGCTTTTGTAACCACTCCCACTAAACTTATTACAT
* 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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