SORCS3 _LIHC.png
Expression analysis of TCGA samples
Basic Information
VIS ID
TVIS10006171
Fusion event
HBV-SORCS3 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
1738
Orient
+
Integrated sequence
TGCCCAAGGTCTTACATAAGAGGACTCTTGGACTCTCAGCAATGTCAACGACCGACCTTGAGGCATACTTCAAAGACTGTTTGTTTAAGGACTGGGAGGA| |GTTGGGGGAGGAGATTAGGTTAAAGGTCTTTGTACTAGGAGGCTGTAGGCATAAATTGGTCTGTTCACCAGCACCATGCAACTTTTTCACCTCTGCCTAA
Host Sequence
Chromosome
chr10
Cytoband
q25.1
Reference genome
GRCh37/hg19
Start
107018647/105258889 (Hg38)
End
107018647/105258889 (Hg38)
Orient
+
Location type
Intron
Fragile sites / regions
FRA10D ; FRA10A ; FRA10B
Target gene
SORCS3
miRNAs that regulate target gene
hsa-mir-335-5p ; hsa-mir-26b-5p
Nearest miRNA
hsa-mir-107/Upstream/990484; hsa-mir-202/Downstream/5639201;
Nearest TSS
ENST00000439456/Upstream/99961; ENST00000424701/Downstream/560308;
Nearest CpG islands
None/Target, chr10-CpG: 68/Upstream/615835, chr10-CpG: 100/Downstream/1905133
Upstream sequence
CACCTTTTCTGTGTCCCTGACAGTGAGTCATGCAGCTGAGGCCACAGGAAATAAACTCCAATCAAACTGGACAATAGCAGCATCAGTTAACAGTAACTAG
Downstream sequence
TCATCAGTTAACCTTTACTTTTCTGGCTCCTTTTCCTGGAAGTTTTACTCCCAATGCTTAAGCCCTTTGGTTGAAATTCTGTGGGATTTTCTTTTATTTT
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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