C12orf40 _LIHC.png
Expression analysis of TCGA samples
Basic Information
VIS ID
TVIS10004870
Fusion event
HBV-C12orf40 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
1829
Orient
+
Integrated sequence
CTGGGAGGAGTTGGGGGAGGAGATTAGGTTAAAGGTCTTTGTACTAGGAGGCTGTAGGCATAAATTGGTCTGTTCACCAGCACCATGCAACTTTTTCACC| |TCTGCCTAATCATCTCATGTTCATGTCCTACTGTTCAAGCCTCCAAGCTGTGCCTTGGGTGGCTTTGGGGCATGGACATTGACCCGTATAAAGAATTTGG
Host Sequence
Chromosome
chr12
Cytoband
q12
Reference genome
GRCh37/hg19
Start
40141121/39747319 (Hg38)
End
40141121/39747319 (Hg38)
Orient
+
Location type
Intronic
Target gene
C12orf40
miRNAs that regulate target gene
hsa-mir-335-5p ; hsa-mir-148b-3p ; hsa-mir-124-3p ; hsa-mir-1-3p
Nearest miRNA
hsa-mir-1244-3/Upstream/13873240; hsa-let-7i/Downstream/2576381;
Nearest TSS
ENST00000382841/Upstream/121101; ENST00000457989/Downstream/88441;
Nearest CpG islands
None/Target, chr12-CpG: 104/Upstream/303622, chr12-CpG: 108/Downstream/357841
Junction sequence
AGACTG
* 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).
Curate