Expression analysis of TCGA samples
Basic Information
VIS ID
TVIS10000165
Fusion event
HBV-SAMD9L integration
Validated
Yes
Detection method
invPCR
Data source
Curated
Sample type
Disease
Hepatocellular carcinoma (HCC)
Quality evaluation
Perfect
Reported year
2018
PubMed ID
Virus Sequence
Virus name
HBV
Reference genome
End
1824
Integrated sequence
TTAAAGACTGGGAGGAGTTGGGGGAGGAGATTAGATTAAAGGTCTTTGTACTAGGAGGCTGTAGGCATAAATTGGTCTGCGCACCAGCACCATGCAACTT| |TTTCACCTCTGCCTAATCATCTCTTGTTCATGTCCTACTGTTCAAGCCTCCAAGCTGTGCCTTGGGTGGCTTTGGGGCATGGACATCGACCCTTATAAAG
Host Sequence
Chromosome
chr7
Cytoband
q21.2
Reference genome
Start
End
93131776 (Hg38)
Orient
+
Location type
Intronic
Target gene
miRNAs that regulate target gene
hsa-mir-146a-5p ; hsa-mir-20a-5p ; hsa-mir-106b-5p ; hsa-mir-6864-3p ; hsa-mir-1273e ; hsa-mir-3672 ; hsa-mir-6502-5p ; hsa-mir-1301-5p ; hsa-mir-873-3p ; hsa-mir-517-5p ; hsa-mir-8067 ; hsa-mir-6508-5p ; hsa-mir-6796-3p ; hsa-mir-574-5p ; hsa-mir-4455 ; hsa-mir-450a-2-3p ; hsa-mir-6857-5p ; hsa-mir-6763-5p ; hsa-mir-3150a-3p ; hsa-mir-6810-5p ; hsa-mir-2110 ; hsa-mir-3147 ; hsa-mir-4425 ; hsa-mir-6867-5p ; hsa-mir-6825-5p ; hsa-mir-939-5p ; hsa-mir-1343-5p ; hsa-mir-3175 ; hsa-mir-8085 ; hsa-mir-6731-5p ; hsa-mir-93-5p ; hsa-mir-519d-3p ; hsa-mir-20b-5p ; hsa-mir-17-5p ; hsa-mir-5192
Nearest miRNA
hsa-mir-10525/Upstream/927678; hsa-mir-10399/Downstream/350984;
Nearest CpG islands
None/Target, chr7-CpG: 39/Upstream/88074, chr7-CpG: 28/Downstream/442997
Nearest cancer related gene
SAMD9L(TSG, No orient, 0)
Downstream sequence
ATTGGTCTGCGCACCAGCACCATGCAACTT
Junction sequence
AACTTGGAGTTGGGCTTTAGACAACTCAGAATTGGTCTGCGCACCAGCACCATGCAACTT
* Color:
Human Sequence
/
Virus Sequence
/
Overlapped sequence
/
Unknown sequence
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).