GDAP1 _LIHC.png
Expression analysis of TCGA samples
Basic Information
VIS ID
TVIS10006216
Fusion event
HBV-GDAP1 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
2892
Orient
+
Integrated sequence
ACACGCAGCGCTTCATTTTGTGGGTCACCATATTCTTGGGAACAAGAGCTACAGCATGGGAGGTTGGTCTTCCAAACCTCGACAAGGCATGGGGACGAAT| |CTTTCTGTTCCCAATCCTCTGGGATTCTTTCCCGATCACCAGTTGGACCCTGCGTTCGGAGCCAACTCAAACAATCCAGATTGGGACTTCAACCCCAACA
Host Sequence
Chromosome
chr8
Cytoband
q21.11
Reference genome
GRCh37/hg19
Start
75376995/74464760 (Hg38)
End
75376995/74464760 (Hg38)
Orient
-
Location type
Intronic
Target gene
GDAP1
miRNAs that regulate target gene
hsa-mir-203a-3p ; hsa-mir-26a-5p ; hsa-mir-200a-3p ; hsa-mir-375 ; hsa-mir-26b-5p ; hsa-mir-17-5p
Nearest miRNA
hsa-mir-124-1/Upstream/10085503; hsa-mir-10400/Downstream/83783;
Nearest TSS
ENST00000518652/Upstream/101809; ENST00000518190/Downstream/135015;
Nearest CpG islands
None/Target, chr8-CpG: 109/Upstream/113951, chr8-CpG: 60/Downstream/519533
Upstream sequence
GGAAGCATCAGTAGAAATGTTATTCATTAAAGACAGTTCAAATAAAAATGAATGTTACTTTTAAGGAACTTATCTTTTACTAAGCATACTTTATAATATC
Downstream sequence
GACAGTCATGCCATATTTAGGGAAAGGGATATTAATTTCATATTCAAACCTAAATACCTGCCTACTGTCATCTTAAATTGTAAGTATCTTCCAAGATACT
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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