SEMA3D _LIHC.png
Expression analysis of TCGA samples
Basic Information
VIS ID
TVIS10006196
Fusion event
HBV-SEMA3D 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
1826
Orient
+
Integrated sequence
GGACTGGGAGGAGTTGGGGGAGGAGATTAGGTTAAAGGTCTTTGTACTAGGAGGCTGTAGGCATAAATTGGTCTGTTCACCAGCACCATGCAACTTTTTC| |ACCTCTGCCTAATCATCTCATGTTCATGTCCTACTGTTCAAGCCTCCAAGCTGTGCCTTGGGTGGCTTTGGGGCATGGACATTGACCCGTATAAAGAATT
Host Sequence
Chromosome
chr7
Cytoband
q21.11
Reference genome
GRCh37/hg19
Start
84643992/85014676 (Hg38)
End
84643992/85014676 (Hg38)
Orient
-
Location type
Intron
Target gene
SEMA3D
miRNAs that regulate target gene
hsa-mir-193a-3p ; hsa-mir-628-5p ; hsa-mir-203a-3p ; hsa-mir-892c-5p ; hsa-mir-302f ; hsa-mir-3646 ; hsa-mir-2053 ; hsa-mir-1468-5p ; hsa-mir-590-3p
Nearest miRNA
hsa-mir-10525/Upstream/9099407; hsa-mir-10399/Downstream/7189339;
Nearest TSS
ENST00000635602/Upstream/74431; ENST00000422448/Downstream/27263;
Nearest CpG islands
None/Target, chr7-CpG: 39/Upstream/74425, chr7-CpG: 94/Downstream/170847
Upstream sequence
TGTGTGAACAGCAGGGGGTTGCAACAGTAAAAGGTTTCTGAGACCTTTTACTCTGAGGATTGTTGATGTAGACTTTCCAAATTAAAAGAGGAGCCCTCAT
Downstream sequence
tatattatttGCAAAACAGTGGGCATCAGTATATACATATTTAGAAATAAGAAATAAGGAAGGAACAATTATAAAAAAGGCAAAATAGTGAATAAAAACA
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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