Basic Information
VIS ID
TVIS20004167
Fusion event
HPV-LINC00486 integration
Validated
Yes
Detection method
APOT and sequencing
Data source
Curated
Sample type
Cell line
Disease
Cervical carcinoma (CC)
Quality evaluation
Good
Reported year
2018
PubMed ID
29364907
Virus Sequence
Virus name
HPV
Subtype
HPV16
Reference genome
AF125673.1
Strand
-
Gene
E7/E1
Start
578
End
1306
Orient
-
Integrated sequence
TACATTGCATGAATATATGTTAGATTTGCAACCAGAGACAACTGATCTCTACTGTTATGAGCAATTAAATGACAGCTCAGAGGAGGAGGATGAAATAGATGGTCCAGCTGGACAAGCAGAACCGGACAGAGCCCATTACAATATTGTAACCTTTTGTTGCAAGTGTGACTCTACGCTTCGGTTGTGCGTACAAAGCACACACGTAGACATTCGTACTTTGGAAGACCTGTTAATGGGCACACTAGGAATTGTGTG
Host Sequence
Chromosome
chr2
Cytoband
p22.3
Reference genome
GRCh37/hg19
Start
33141280/32916213 (Hg38)
End
33141692/32916625 (Hg38)
Orient
-
Location type
Intronic
Target gene
LINC00486
Nearest miRNA
hsa-mir-1301/Upstream/280882; hsa-mir-10b/Downstream/501891;
Nearest TSS
ENST00000437798/Upstream/33412; ENST00000440786/Downstream/10502;
Nearest CpG islands
None/Target, chr2-CpG: 135/Upstream/288010, chr2-CpG: 164/Downstream/29756
Nearby gene
TTC27(-95162) ; LOC100271832(+10501) ;
Upstream sequence
GATCAAGGGGGCTAGGAGGGTTACAGAAATGGGGGGCAGCTTGAGCTGAGACTGCTCACACGGCTATCTCTGCCCATGTGACTTGCCCCCTCTTGACAGT
Downstream sequence
NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN
Target sequence
Cgggggggcgtgggtagggggggggggtggggggggggcgggggggggggggggggggggggggggggggggggggggggggggggggggggggggggggggggggggggggggggggggagggaggggggggtgagagggggggggggggggggggggggggggggggggggggggggggggggggagggggggggggggggggggggggggggggggggggggggaggggggggggggggggggggggggggg
Reference
Warburton, A., et al. HPV integration hijacks and multimerizes a cellular enhancer to generate a viral-cellular super-enhancer that drives high viral oncogene expression. PLoS Genet ,2018,14(1): e1007179.
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