GATC _LIHC.png
Expression analysis of TCGA samples
Basic Information
VIS ID
TVIS10010333
Fusion event
HBV-GATC integration
Validated
No
Detection method
NGS
Data source
Curated
Sample type
Tumor
Disease
Hepatocellular carcinoma (HCC)
Quality evaluation
Normal
Reported year
2018
PubMed ID
30271481
Virus Sequence
Virus name
HBV
Reference genome
NC_003977
Region type
Polymerase|large S protein|middle S protein|
Start
26
Orient
+
Integrated sequence
AATTCCACAACCTTCCACCAAACTCT| |GCAAGATCCCAGAGTGAGAGGCCTGTATTTCCCTGCTGGTGGCTCCAGTTCAGGAACAGTAAACCCTGTTCTGACTACTGCCTCTCCCTTATCGTCAATC
Host Sequence
Chromosome
chr12
Cytoband
q24.31
Reference genome
GRCh37/hg19
Start
120885965/120448162 (Hg38)
End
120885965/120448162 (Hg38)
Orient
-
Location type
Intronic
Fragile sites / regions
FRA12E ; FRA12C
Target gene
GATC
miRNAs that regulate target gene
hsa-mir-30a-5p ; hsa-let-7b-5p ; hsa-mir-4279 ; hsa-mir-6778-3p ; hsa-mir-1976 ; hsa-mir-3653-5p ; hsa-mir-6747-3p ; hsa-mir-6727-3p ; hsa-mir-4722-3p ; hsa-mir-6827-3p ; hsa-mir-340-3p ; hsa-mir-4532 ; hsa-mir-1247-3p ; hsa-mir-4740-3p ; hsa-mir-122-3p
Nearest miRNA
hsa-let-7i/Upstream/292663; hsa-mir-3612/Downstream/275031;
Nearest TSS
ENST00000382841/Upstream/1585; ENST00000549649/Downstream/15234;
Nearest CpG islands
None/Target, chr12-CpG: 104/Upstream/1262, chr12-CpG: 121/Downstream/20713
Upstream sequence
TCTTTCAAATGTCTTCTCTACTTTGCAAttttctttttcctttgggacggggtctcactatgttgcccaggctggtcgcaaacttctagactcaagagat
Downstream sequence
cctcctgcctcagcctcccaaatagctgggactataggtgtgcaccaccacacctggctaatacttaaaatttttgtagaaacggggtcttgccatgttg
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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