GSDMC _LIHC.png
Expression analysis of TCGA samples
Basic Information
VIS ID
TVIS10005064
Fusion event
HBV-GSDMC integration
Validated
No
Detection method
PCR and Ultra-deep sequencing
Data source
Curated
Sample type
Nontumor
Disease
Hepatocellular carcinoma (HCC)
Quality evaluation
Normal
Reported year
2018
PubMed ID
29861854
Virus Sequence
Virus name
HBV
Reference genome
AP011098
Start
845
Orient
-
Integrated sequence
ATGTGGTATTGGGGGCCAAGTCTGTACAACATCTTGAGTCCCTTTTTACCTCTATTACCAATTTTCTTTTGTCTTTGGGTATACATTTGAACCCTAATAA| |AACCAAACGTTGGGGCTACTCCCTTAACTTCATGGGATATGTAATTGGAAGTTGGGGTACTTTACCACAGGAACATATTGTACGGAAACTCAAGCAATGT
Host Sequence
Chromosome
chr8
Cytoband
q24.21
Reference genome
GRCh37/hg19
Start
130795530/129783284 (Hg38)
End
130795530/129783284 (Hg38)
Orient
+
Location type
Intron
Target gene
GSDMC
Nearest miRNA
hsa-mir-1204/Upstream/299142; hsa-mir-10400/Downstream/225050;
Nearest TSS
ENST00000518652/Upstream/5697; ENST00000524100/Downstream/3604;
Nearest CpG islands
None/Target, chr8-CpG: 109/Upstream/1933306, chr8-CpG: 122/Downstream/155842
Upstream sequence
ctctatctctgggttctctgttctcatttcttagtctatatgtctctcctctgccaataccatgcatccttgactactgtaattatataagaagttgaga
Downstream sequence
aaaggaagaagtcaaattgtccttgtttgtggatgatgtggtcttatatatggaacaaactgaagattccaacaacaaaaaactattagaagttataaat
Reference
Tu, T., et al. Hepatitis B Virus DNA Integration Occurs Early in the Viral Life Cycle in an In Vitro Infection Model via Sodium Taurocholate Cotransporting Polypeptide-Dependent Uptake of Enveloped Virus Particles. J Virol ,2018,92(11).
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