COL4A6 _LIHC.png
Expression analysis of TCGA samples
Basic Information
VIS ID
TVIS10007982
Fusion event
HBV-COL4A6 integration
Validated
No
Detection method
NGS
Data source
Curated
Sample type
Nontumor
Disease
Hepatocellular carcinoma (HCC)
Quality evaluation
Normal
Reported year
2018
PubMed ID
30271481
Virus Sequence
Virus name
HBV
Reference genome
NC_003977
Region type
precore/core protein|Core and e antigen|
Start
1996
Orient
+
Integrated sequence
TGGGGCATGGACATCGACCCTTATAAAGAATTTGGAGCTACTGTGGAGTTACTCTCGTTTTTGCCTTCTGACTTCTTTCCTTCAGTACGAGATCTTCTAG| |ATACCGCCTCAGCTCTGTATCGGGAAGCCTTAGAGTCTCCTGAGCATTGTTCACCTCACCATACTGCACTCAGGCAAGCAATTCTTTGCTGGGGGGAACT
Host Sequence
Chromosome
chrX
Cytoband
q22.3
Reference genome
GRCh37/hg19
Start
107425500/108182270 (Hg38)
End
107425500/108182270 (Hg38)
Orient
-
Location type
Intronic
Target gene
COL4A6
miRNAs that regulate target gene
hsa-mir-197-3p ; hsa-mir-29b-3p
Nearest miRNA
hsa-let-7f-2/Upstream/1542374; hsa-mir-105-1/Downstream/1873059;
Nearest TSS
ENST00000429181/Upstream/18672; ENST00000477429/Downstream/256160;
Nearest CpG islands
None/Target, chrX-CpG: 62/Upstream/90361, chrX-CpG: 31/Downstream/550359
Upstream sequence
ttaggggttagggttagggttaggggttagggttagggttaggggttaggggttaggggttaggggttagggtagggtagggtagggtagggagggttag
Downstream sequence
tctggtacatgctcaattaataatagttcttattATCTTGAACTATTATCTTATGTAAGAATGAGTACTCAGTAGAGCTCCTGCAAGGCCATCCTCAGGT
Reference
Yang, L., et al. Molecular Characterization of HBV DNA Integration in Patients with Hepatitis and Hepatocellular Carcinoma. J Cancer ,2018,9(18): 3225-3235.
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