SMARCB1 _LIHC.png
Expression analysis of TCGA samples
Basic Information
VIS ID
TVIS10005869
Fusion event
HBV-SMARCB1 integration
Validated
No
Detection method
PCR and Ultra-deep sequencing
Data source
Curated
Sample type
Tumor
Disease
Hepatocellular carcinoma (HCC)
Quality evaluation
Normal
Reported year
2018
PubMed ID
29861854
Virus Sequence
Virus name
HBV
Reference genome
AP011098
Start
2929
Orient
-
Integrated sequence
GGGAACAAGAGCTACAGCATGGGAGGTTGGTCTTCCAAACCTCGACAAGGCATGGGGACGAATCTTTCTGTTCCCAATCCTCTGGGATTCTTTCCCGATC| |ACCAGTTGGACCCTGCGTTCGGAGCCAACTCAAACAATCCAGATTGGGACTTCAACCCCAACAAGGATCACTGGCCAGAGGCAAATCAGGTAGGAGCGGG
Host Sequence
Chromosome
chr22
Cytoband
q11.23
Reference genome
GRCh37/hg19
Start
24151748/23809561 (Hg38)
End
24151748/23809561 (Hg38)
Orient
-
Location type
Intron
Target gene
SMARCB1
miRNAs that regulate target gene
hsa-mir-192-5p ; hsa-mir-1-3p ; hsa-mir-215-5p ; hsa-let-7b-5p ; hsa-mir-671-5p ; hsa-mir-381-3p ; hsa-mir-206 ; hsa-mir-218-5p
Nearest miRNA
hsa-mir-1286/Upstream/923182; hsa-let-7a-3/Downstream/1646085;
Nearest TSS
ENST00000624155/Upstream/7014; ENST00000477836/Downstream/5430;
Nearest CpG islands
None/Target, chr22-CpG: 279/Upstream/36281, chr22-CpG: 107/Downstream/28743
Nearest cancer related gene
SMARCB1(TSG, No orient, 0)
Upstream sequence
agaggggtttctccatgttggtcaggctggccttgaactccccacctcaggtgatccgcccacctcggcctcccaaagtgctgggattacaggcgtgagc
Downstream sequence
cactgtgctcggccaattttttgtattttttagtagagacggggtttcactgtgttagccaggatggtctcgatctcctgacctcgtgttccgcccgcct
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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