HSDL2 _LIHC.png
Expression analysis of TCGA samples
Basic Information
VIS ID
TVIS10004809
Fusion event
HBV-HSDL2 integration
Validated
No
Detection method
PCR and Ultra-deep sequencing
Data source
Curated
Sample type
Tumor
Disease
Hepatocellular carcinoma (HCC)
Quality evaluation
Normal
Reported year
2018
PubMed ID
29861854
Virus Sequence
Virus name
HBV
Reference genome
AP011098
Start
1397
Orient
+
Integrated sequence
CTCGCAGCCGGTCTGGAGCAAAACTTATCGGGACTGACAACTCTGTTGTCCTCTCTCGGAAATACACCTCCTTCCCATGGCTGCTCGGGTGTGCTGCCAA| |CTGGATCCTGCGCGGGACGTCCTTTGTCTACGTCCCGTCGGCGCTGAATCCCGCGGACGACCCGTCTCGGGGCCGTTTGGGGCTCTACCGTCCCCTTCTT
Host Sequence
Chromosome
chr9
Cytoband
q32
Reference genome
GRCh37/hg19
Start
115157931/112395651 (Hg38)
End
115157931/112395651 (Hg38)
Orient
-
Location type
Intron
Fragile sites / regions
FRA9E
Target gene
HSDL2
miRNAs that regulate target gene
hsa-mir-16-5p ; hsa-mir-15a-5p ; hsa-mir-328-3p ; hsa-mir-3121-3p ; hsa-mir-577
Nearest miRNA
hsa-let-7a-1/Upstream/463482; hsa-mir-12126/Downstream/1813783;
Nearest TSS
ENST00000422679/Upstream/15529; ENST00000480881/Downstream/18351;
Nearest CpG islands
None/Target, chr9-CpG: 64/Upstream/15293, chr9-CpG: 135/Downstream/90797
Upstream sequence
aggcaatcaactgggaacagaaagacctttcacaaatggtgctgtgaaaattagaaatccacaaggaaaagcaaaaaaaaagcatctttccttccctcac
Downstream sequence
aactatgagaggccaattcttaggtattaaaggaggggcaggcatgccaggttggacggctcccataggtttaattacagcattaatggcccttaaagca
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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