Basic Information
VIS ID
TVIS20001736
Fusion event
HPV-RARB integration
Validated
No
Detection method
HIVID
Data source
Curated
Sample type
Tumor
Disease
Not given
Quality evaluation
Normal
Reported year
2015
PubMed ID
25581428
Virus Sequence
Virus name
HPV
Subtype
HPV16
Reference genome
NC_001526.2
Host Sequence
Chromosome
chr3
Cytoband
p24.2
Reference genome
GRCh37/hg19
Start
25321952/25280461 (Hg38)
End
25321952/25280461 (Hg38)
Location type
Intronic
Fragile sites / regions
FRA3A
Target gene
RARB
miRNAs that regulate target gene
hsa-mir-16-2-3p ; hsa-mir-30c-5p ; hsa-mir-15a-5p ; hsa-mir-16-5p ; hsa-mir-33a-3p ; hsa-mir-15b-5p ; hsa-mir-195-5p ; hsa-mir-424-5p ; hsa-mir-497-5p ; hsa-mir-545-5p ; hsa-mir-4307 ; hsa-mir-6792-5p ; hsa-mir-6838-5p ; hsa-let-7c-5p ; hsa-mir-548c-3p ; hsa-mir-548x-3p ; hsa-mir-548j-3p ; hsa-mir-548aq-3p ; hsa-mir-548am-3p ; hsa-mir-548aj-3p ; hsa-mir-548ah-3p ; hsa-mir-548ae-3p ; hsa-mir-578 ; hsa-mir-1-3p ; hsa-mir-106a-5p ; hsa-mir-146a-5p ; hsa-mir-146b-5p
Nearest miRNA
hsa-mir-12127/Upstream/5142820; hsa-let-7g/Downstream/384412;
Nearest TSS
ENST00000440867/Upstream/106129; ENST00000489694/Downstream/147802;
Nearest CpG islands
None/Target, chr3-CpG: 148/Upstream/449861, chr3-CpG: 125/Downstream/383604
Nearest cancer related gene
RARB(TSG, No orient, 0)
Upstream sequence
aatttttatttcaccaataatgaatgaccgacccttcatagcaccctcgtcaacattAGATTATTGCTTATATTATGTCAAAAACTGACATCATTGTTTT
Downstream sequence
tgaaacgctgagtgaaatgacctggacataaacctccttaggaatgcttagaaatgttggaaaggtcactagacttttcacagaacatggggtattgggt
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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