RGS12 _LIHC.png
Expression analysis of TCGA samples
Basic Information
VIS ID
TVIS10005683
Fusion event
HBV-RGS12 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
2382
Orient
-
Integrated sequence
CTCCTCCCGCTTACAGACCACCAAATGCCCCTATCTTATCAACACTTCCGGAAACTACTGTTGTTAGACGACGAGGCAGGTCCCCTAGAAGAAGAACTCC| |CTCGCCTCGCAGACGAAGGTCTCAATCGCCGCGTCGCAGAAGATCTCAATCTCGGGAATCTCAATGTTAGTATCCCTTGGACTCATAAGGTGGGAAACTT
Host Sequence
Chromosome
chr4
Cytoband
p16.3
Reference genome
GRCh37/hg19
Start
3421873/3420146 (Hg38)
End
3421873/3420146 (Hg38)
Orient
-
Location type
Intron
Target gene
RGS12
miRNAs that regulate target gene
hsa-mir-149-5p ; hsa-mir-138-5p ; hsa-mir-7704 ; hsa-mir-4532 ; hsa-mir-4726-3p ; hsa-mir-6764-5p ; hsa-mir-1915-3p ; hsa-mir-6840-3p ; hsa-mir-665 ; hsa-mir-4459
Nearest miRNA
hsa-mir-4800/Upstream/1169990; hsa-mir-12113/Downstream/2503129;
Nearest TSS
ENST00000502981/Upstream/2633; ENST00000510803/Downstream/242;
Nearest CpG islands
None/Target, chr4-CpG: 46/Upstream/6520, chr4-CpG: 24/Downstream/27777
Junction sequence
AT
* 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).
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