FGA _LIHC.png
Expression analysis of TCGA samples
Basic Information
VIS ID
TVIS10005139
Fusion event
HBV-FGA 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
1801
Orient
+
Integrated sequence
CATACTTCAAAGACTGTTTGTTTAAGGACTGGGAGGAGTTGGGGGAGGAGATTAGGTTAAAGGTCTTTGTACTAGGAGGCTGTAGGCATAAATTGGTCTG| |TTCACCAGCACCATGCAACTTTTTCACCTCTGCCTAATCATCTCATGTTCATGTCCTACTGTTCAAGCCTCCAAGCTGTGCCTTGGGTGGCTTTGGGGCA
Host Sequence
Chromosome
chr4
Cytoband
q31.3
Reference genome
GRCh37/hg19
Start
155506454/154585302 (Hg38)
End
155506454/154585302 (Hg38)
Orient
+
Location type
FGA,intron FGA,exon
Target gene
FGA
miRNAs that regulate target gene
hsa-mir-409-3p ; hsa-mir-29c-3p ; hsa-mir-144-3p ; hsa-mir-29a-3p ; hsa-mir-29b-3p
Nearest miRNA
hsa-mir-12113/Upstream/2048786; hsa-mir-1305/Downstream/4543500;
Nearest TSS
ENST00000502981/Upstream/19521; ENST00000500890/Downstream/5442;
Nearest CpG islands
None/Target, chr4-CpG: 46/Upstream/34772, chr4-CpG: 39/Downstream/41530
Upstream sequence
tggtcacgtacaaaagatgattctaaagcatgtctgacatgttaaatgaacaatatccaaaactcttgagaaagaagctcaatgagtgagaactgccttc
Downstream sequence
tgagtcatggctctgtactgttaggcatttgggaatacagagatgagacagacaaaggccctgcccccaaggaacttacagtctagcacaaaaacagacc
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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