SPI1 _LIHC.png
Expression analysis of TCGA samples
Basic Information
VIS ID
TVIS10005380
Fusion event
HBV-SPI1 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
2101
Orient
-
Integrated sequence
CTCTGCTCTGTATCGGGAGGCCTTAGAGTCTCCGGAACATTGTTCACCTCACCATACAGCACTCAGGCAAGCTATTCTGTGTTGGGGTGAGTTGATGAAT| |CTGGCCACCTGGGTGGGAAGTAATTTGGAAGACCCAGCATCCAGGGAATTAGTAGTCAGCTATGTCAATGTTAATATGGGCCTAAAAATCAGACAACTAT
Host Sequence
Chromosome
chr11
Cytoband
p11.2
Reference genome
GRCh37/hg19
Start
47384375/47362824 (Hg38)
End
47384375/47362824 (Hg38)
Orient
-
Location type
Intron
Target gene
SPI1
miRNAs that regulate target gene
hsa-mir-155-5p ; hsa-mir-569 ; hsa-mir-34a-5p ; hsa-mir-424-5p ; hsa-mir-9-5p ; hsa-mir-296-3p ; hsa-mir-6845-3p ; hsa-mir-6749-3p ; hsa-mir-4669 ; hsa-mir-3657 ; hsa-mir-6090 ; hsa-mir-7113-3p ; hsa-mir-339-5p ; hsa-mir-1247-3p ; hsa-mir-5587-3p
Nearest miRNA
hsa-mir-129-2/Upstream/183087; hsa-let-7a-2/Downstream/38146;
Nearest TSS
ENST00000527297/Upstream/10122; ENST00000527091/Downstream/15567;
Nearest CpG islands
None/Target, chr11-CpG: 30/Upstream/7027, chr11-CpG: 16/Downstream/15413
Nearest cancer related gene
SPI1(OG, No orient, 0)
Upstream sequence
accaccatgcccagctaatttttgtatttttagtagagatggggtttcactatattggccaggctggtcttgatctcctgacctcgtgatctgcccacct
Downstream sequence
cagcctcccaaagtgctgggattacaggcttgagccactgcgcccagcTGAGACCCTGTCTCTTAACAAAAAAGTATTCAGTGTGCAGGGGGAGGGGCTT
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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