Expression analysis of TCGA samples
Basic Information
VIS ID
TVIS10004829
Fusion event
HBV-chr1 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
1822
Orient
+
Integrated sequence
TTAAGGACTGGGAGGAGTTGGGGGAGGAGATTAGGTTAAAGGTCTTTGTACTAGGAGGCTGTAGGCATAAATTGGTCTGTTCACCAGCACCATGCAACTT| |TTTCACCTCTGCCTAATCATCTCATGTTCATGTCCTACTGTTCAAGCCTCCAAGCTGTGCCTTGGGTGGCTTTGGGGCATGGACATTGACCCGTATAAAG
Host Sequence
Chromosome
chr1
Cytoband
q21.2
Reference genome
End
144851662/149032779 (Hg38)
Orient
-
Location type
Exon
Fragile sites / regions
miRNAs that regulate target gene
hsa-mir-505-3p ; hsa-mir-92a-3p ; hsa-let-7a-5p ; hsa-mir-493-3p ; hsa-mir-620 ; hsa-mir-1270 ; hsa-mir-4531 ; hsa-mir-5703 ; hsa-mir-4516 ; hsa-mir-4434 ; hsa-mir-539-5p ; hsa-mir-432-5p ; hsa-mir-3976 ; hsa-mir-6856-5p ; hsa-mir-6758-5p ; hsa-mir-3121-3p ; hsa-mir-452-3p ; hsa-mir-582-5p ; hsa-mir-3618 ; hsa-mir-139-5p ; hsa-mir-670-3p ; hsa-mir-4465 ; hsa-mir-26b-5p ; hsa-mir-26a-5p ; hsa-mir-1297 ; hsa-mir-3667-3p ; hsa-mir-6734-3p ; hsa-mir-660-3p ; hsa-mir-5193 ; hsa-mir-6513-3p ; hsa-mir-8079 ; hsa-mir-1245a ; hsa-mir-3614-3p
Nearest miRNA
hsa-mir-101-1/Upstream/644416; hsa-mir-1182/Downstream/1459566;
Nearest CpG islands
None/Target, chr1-CpG: 111/Upstream/79630, chr1-CpG: 98/Downstream/70133
Upstream sequence
ATATCATATATTTATACACACAAACACATTCTACCAGCACTGTGAAGACACAGACTAGGCTTTACTAGGCTTGGGGCCTCTCCCATGCCACTTAAAAATG
Downstream sequence
AGCACAGGTTTGCTCTATGCAAGAATTTCAACAGAGTTGGTCTGGCCATCAGTCTGCAATTTCCCCGAGATAAGATAGGGTGACAAAATGGGACAGCAAC
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).