SLC38A4 _LIHC.png
Expression analysis of TCGA samples
Basic Information
VIS ID
TVIS10005773
Fusion event
HBV-SLC38A4 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
1790
Orient
+
Integrated sequence
CGACCTTGAGGCATACTTCAAAGACTGTTTGTTTAAGGACTGGGAGGAGTTGGGGGAGGAGATTAGGTTAAAGGTCTTTGTACTAGGAGGCTGTAGGCAT| |AAATTGGTCTGTTCACCAGCACCATGCAACTTTTTCACCTCTGCCTAATCATCTCATGTTCATGTCCTACTGTTCAAGCCTCCAAGCTGTGCCTTGGGTG
Host Sequence
Chromosome
chr12
Cytoband
q13.11
Reference genome
GRCh37/hg19
Start
47183940/46790157 (Hg38)
End
47183940/46790157 (Hg38)
Orient
+
Location type
Intron
Fragile sites / regions
FRA12A
Target gene
SLC38A4
miRNAs that regulate target gene
hsa-mir-335-5p ; hsa-mir-6858-5p ; hsa-mir-4689 ; hsa-mir-6739-5p ; hsa-mir-3153 ; hsa-mir-6733-5p ; hsa-mir-4763-3p ; hsa-mir-1207-5p ; hsa-mir-1255b-5p ; hsa-mir-1255a ; hsa-mir-139-3p ; hsa-mir-6722-3p ; hsa-mir-1909-3p ; hsa-mir-4784 ; hsa-mir-3150b-3p ; hsa-mir-6783-5p
Nearest miRNA
hsa-mir-1244-3/Upstream/4466298; hsa-let-7i/Downstream/397655;
Nearest TSS
ENST00000382841/Upstream/20853; ENST00000621214/Downstream/35828;
Nearest CpG islands
None/Target, chr12-CpG: 104/Upstream/406084, chr12-CpG: 64/Downstream/40972
Upstream sequence
acaagagtgaaactctgtctGTCTCAATAAATAAATAAATAAACCTTAGAAATAAAATAGAAAATAATTATTGTAGGAGATCTGTACAAGCTATTTTTTA
Downstream sequence
TAACAGAAGCTAATCCTGAAAATAATCTGGAGAGGAAAGAGGATGACAGGGTTACTTTTTGAGAATAGAAAACAGTATGAGATGTAGATAGAAACAGCAC
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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