Expression analysis of TCGA samples
Basic Information
VIS ID
TVIS20000059
Fusion event
HPV-DMRT1 integration
Validated
Yes
Detection method
PCR and Sanger sequencing
Data source
Curated
Sample type
Disease
Cervical carcinoma (CC)
Quality evaluation
Normal
Reported year
2016
PubMed ID
Virus Sequence
Virus name
HPV
Subtype
HPV16
Reference genome
Region type
E2/E4
Start
3611
Integrated sequence
AATATGGAAGTATGGGTGTATTTTTTGGTGGGTTAGGAATTGGAACAGGGTCGGGTACAGGCGGACGCACTGGGTATATTCCATTGGGAACAAGGCCTCC| |CACAGCTACAGATACACTTGCTCCTGTAAGACCCCCTTTAACAGTAGATCCTGTGGGCCCTTCTGATCCTTCTATAGTTTCTTTAGTGGAAGAAACTAGT
Host Sequence
Chromosome
chr9
Cytoband
p24.3
Reference genome
Start
End
873456/873456 (Hg38)
Location type
Intronic
Target gene
Nearest miRNA
hsa-mir-1302-9/Upstream/843175; hsa-let-7a-1/Downstream/3976841;
Nearest CpG islands
None/Target, chr9-CpG: 64/Upstream/30092, chr9-CpG: 98/Downstream/96141
Upstream sequence
tgcacttccagatactacaaaaagagtgtttcaaacctgctctatgaaagggaatgttcaactctgtgacttgaatgcaaacatcacagagatgtttctg
Downstream sequence
GCACAAATGTTCAGTGTTCTTTTGAACTCAATTCCTTTAAGTAGTCACCATTTCCATAAATGCTAATTGTTGTAATGATTGAATAAATATGGTAAAATAT
Reference
Liu, Y., et al. Comprehensive mapping of the human papillomavirus (HPV) DNA integration sites in cervical carcinomas by HPV capture technology. Oncotarget,2016, 7(5): 5852-5864.