hsa-mir-187-5p _LIHC.png
EFCAB1 _LIHC.png
Expression analysis of TCGA samples
Basic Information
VIS ID
TVIS10004697
Fusion event
HBV-EFCAB1 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
2741
Orient
-
Integrated sequence
TGCTAGGTTCTATCCTAACCTTACCAAATATTTGCCCTTGGATAAAGGCATTAAACCTTATTATCCTGAACATGCAGTTAATCATTACTTCAAAACTAGG| |CATTATTTACATACTCTGTGGAAGGCTGGCATTCTATATAAGAGAGAAACTACACGCAGCGCTTCATTTTGTGGGTCACCATATTCTTGGGAACAAGAGC
Host Sequence
Chromosome
chr8
Cytoband
q11.21
Reference genome
GRCh37/hg19
Start
49642747/48730188 (Hg38)
End
49642747/48730188 (Hg38)
Orient
-
Location type
Intron
Target gene
EFCAB1
miRNAs that regulate target gene
hsa-mir-1-3p ; hsa-mir-328-3p ; hsa-mir-4639-5p ; hsa-mir-4745-3p ; hsa-mir-1538 ; hsa-mir-4749-3p ; hsa-mir-6769a-3p ; hsa-mir-527 ; hsa-mir-518a-5p ; hsa-mir-187-5p ; hsa-mir-494-3p
Nearest miRNA
hsa-mir-124-1/Upstream/5833913; hsa-mir-10400/Downstream/12984600;
Nearest TSS
ENST00000518652/Upstream/63; ENST00000522267/Downstream/422;
Nearest CpG islands
None/Target, chr8-CpG: 109/Upstream/173753, chr8-CpG: 37/Downstream/4955
Upstream sequence
tgggcgactgagctcaagcatctgcactaagaggcaaaatgacagagtttaactggtatgtgaccttcctctgggggaacactccactggtaagggaaaa
Downstream sequence
AGAACACTTGAATCAATATTCTCTAGTTTTATGGTTACAATTCAAGTAATGAAATCTGTCAAATGCTTAACATATAAATGTATATGTACATAATTAGCAT
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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