SLC8A3 _LIHC.png
Expression analysis of TCGA samples
Basic Information
VIS ID
TVIS10005859
Fusion event
HBV-SLC8A3 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
2444
Orient
+
Integrated sequence
GTTAGACGACGAGGCAGGTCCCCTAGAAGAAGAACTCCCTCGCCTCGCAGACGAAGGTCTCAATCGCCGCGTCGCAGAAGATCTCAATCTCGGGAATCTC| |AATGTTAGTATCCCTTGGACTCATAAGGTGGGAAACTTTACTGGGCTTTATTCTTCTACTGTACCTGTCTTTAATCCTGAGTGGCAAACTCCCTCCTTTC
Host Sequence
Chromosome
chr14
Cytoband
q24.2
Reference genome
GRCh37/hg19
Start
70582836/70116119 (Hg38)
End
70582836/70116119 (Hg38)
Orient
-
Location type
Intron
Fragile sites / regions
FRA14C
Target gene
SLC8A3
miRNAs that regulate target gene
hsa-mir-874-5p ; hsa-mir-5699-5p ; hsa-mir-298 ; hsa-mir-5008-5p ; hsa-mir-6868-5p ; hsa-mir-8073 ; hsa-mir-221-5p ; hsa-mir-186-3p ; hsa-mir-759 ; hsa-mir-4257 ; hsa-mir-6847-5p ; hsa-mir-5000-5p ; hsa-mir-6769a-3p
Nearest miRNA
hsa-mir-208a/Upstream/2674189; hsa-mir-1185-1/Downstream/2400701;
Nearest TSS
ENST00000550708/Upstream/35913; ENST00000554008/Downstream/52365;
Nearest CpG islands
None/Target, chr14-CpG: 35/Upstream/69842, chr14-CpG: 22/Downstream/71522
Upstream sequence
TTTCTCAAAGGAATGCCTAGGCTTTTATTTTGCAACAGGAGATGATGAGAAGAAAGAGAATTGGCACCCCCCTCCCCCACAAAGGGAGGTAGTGCTGAAA
Downstream sequence
GCTCAGAGAGGGGGTCATAGACTTTGAACTTGGATGTAGCCTGGGCCGGGGTGGCTGGGGAAATAATAAATATGGCGCTTGGGTCTTCCTGACTCTCCTC
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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