Expression analysis of TCGA samples
Basic Information
VIS ID
TVIS10006298
Fusion event
HBV-RIMS4 integration
Validated
No
Detection method
PCR and Ultra-deep sequencing
Data source
Curated
Sample type
Disease
Hepatocellular carcinoma (HCC)
Quality evaluation
Normal
Reported year
2018
PubMed ID
Virus Sequence
Virus name
HBV
Reference genome
Start
1791
Orient
+
Integrated sequence
GACCTTGAGGCATACTTCAAAGACTGTTTGTTTAAGGACTGGGAGGAGTTGGGGGAGGAGATTAGGTTAAAGGTCTTTGTACTAGGAGGCTGTAGGCATA| |AATTGGTCTGTTCACCAGCACCATGCAACTTTTTCACCTCTGCCTAATCATCTCATGTTCATGTCCTACTGTTCAAGCCTCCAAGCTGTGCCTTGGGTGG
Host Sequence
Chromosome
chr20
Cytoband
q13.12
Reference genome
Start
End
43413283/44784642 (Hg38)
Orient
+
Location type
Intron
Target gene
miRNAs that regulate target gene
hsa-mir-186-5p ; hsa-mir-125b-5p ; hsa-mir-1304-5p ; hsa-mir-6765-5p ; hsa-mir-3188 ; hsa-mir-6884-5p ; hsa-mir-485-5p ; hsa-mir-3975 ; hsa-mir-2467-5p ; hsa-mir-6128 ; hsa-mir-1976 ; hsa-mir-3653-5p ; hsa-mir-4254 ; hsa-mir-3690 ; hsa-mir-1-3p ; hsa-mir-206 ; hsa-mir-613 ; hsa-mir-4753-3p ; hsa-mir-6873-3p ; hsa-mir-340-5p ; hsa-mir-130b-5p ; hsa-mir-7110-3p ; hsa-mir-5590-3p ; hsa-mir-142-5p ; hsa-mir-1305 ; hsa-mir-421 ; hsa-mir-4775 ; hsa-mir-505-3p ; hsa-mir-548ae-3p ; hsa-mir-548ah-3p ; hsa-mir-548aj-3p ; hsa-mir-548am-3p ; hsa-mir-548aq-3p ; hsa-mir-548j-3p ; hsa-mir-548x-3p ; hsa-mir-5582-3p ; hsa-mir-7159-5p
Nearest miRNA
hsa-mir-103a-2/Upstream/376439; hsa-mir-1-1/Downstream/640868;
Nearest CpG islands
None/Target, chr20-CpG: 39/Upstream/33845, chr20-CpG: 103/Downstream/25454
Junction sequence
G
* 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).