TSPAN9 _LIHC.png
Expression analysis of TCGA samples
Basic Information
VIS ID
TVIS10005183
Fusion event
HBV-TSPAN9 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
664
Orient
-
Integrated sequence
TTGCTGTACAAAACCTTCGGACGGAAACTGCACTTGTATTCCCATCCCATCATCCTGGGCTTTCGCAAGATTCCTATGGGAGTGGGCCTCAGTCCGTTTC| |TCCTGGCTCAGTTTACTAGTGCCATTTGTTCAGTGGTTCGTAGGGCTTTCCCCCACTGTTTGGCTTTCAGTTATATGGATGATGTGGTATTGGGGGCCAA
Host Sequence
Chromosome
chr12
Cytoband
p13.32
Reference genome
GRCh37/hg19
Start
3340555/3231389 (Hg38)
End
3340555/3231389 (Hg38)
Orient
-
Location type
Intron
Target gene
TSPAN9
miRNAs that regulate target gene
hsa-mir-1180-3p ; hsa-mir-320a ; hsa-mir-4258 ; hsa-mir-6089 ; hsa-mir-6859-3p ; hsa-mir-7108-3p
Nearest miRNA
hsa-mir-3649/Upstream/1571009; hsa-let-7i/Downstream/3732310;
Nearest TSS
ENST00000382841/Upstream/16138; ENST00000492305/Downstream/41523;
Nearest CpG islands
None/Target, chr12-CpG: 104/Upstream/30285, chr12-CpG: 72/Downstream/134455
Upstream sequence
cctttttgggcctcagaattcctgtcagtTCACTTGAGCCCTAGGATACCTCTAGGCAGAAAATTCTGGTCCTGCTGTCACCACTGAAGACATCAAACAT
Downstream sequence
GCTCTGAGATGGGGAGTCAGCGAAGACAGCACTCCAGGCTGGACCTGGCCCCAGCCCGAACAGTCCTGCATCAGCCCCGCGTCACTACGGAGAGATGCCG
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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