RALGDS _LIHC.png
Expression analysis of TCGA samples
Basic Information
VIS ID
TVIS10010296
Fusion event
HBV-RALGDS 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
1990
Orient
+
Integrated sequence
TGGCTTTGGGGCATGGACATCGACCCTTATAAAGAATTTGGAGCTACTGTGGAGTTACTCTCGTTTTTGCCTTCTGACTTCTTTCCTTCAGTACGAGATC| |TTCTAGATACCGCCTCAGCTCTGTATCGGGAAGCCTTAGAGTCTCCTGAGCATTGTTCACCTCACCATACTGCACTCAGGCAAGCAATTCTTTGCTGGGG
Host Sequence
Chromosome
chr9
Cytoband
q34.2
Reference genome
GRCh37/hg19
Start
135981586/133106199 (Hg38)
End
135981586/133106199 (Hg38)
Orient
+
Location type
Intronic
Target gene
RALGDS
miRNAs that regulate target gene
hsa-mir-335-5p ; hsa-mir-615-3p ; hsa-mir-186-5p ; hsa-mir-183-5p ; hsa-mir-374a-5p
Nearest miRNA
hsa-let-7a-1/Upstream/54140; hsa-mir-126/Downstream/1273212;
Nearest TSS
ENST00000422679/Upstream/1597; ENST00000426651/Downstream/1819;
Nearest CpG islands
None/Target, chr9-CpG: 64/Upstream/34536, chr9-CpG: 113/Downstream/14383
Nearest cancer related gene
RALGDS(OG, No orient, 0)
Upstream sequence
catccatgccagtatctactggattttttaaattttttttattatgtccatttttgcagaagtaaggtggtattgcattgtggtttcgatttgcatttcc
Downstream sequence
CATTCCCGTTTCCACTGAGCAGCTATTTCCAAAGGGGtttttttctttttttggagacagtttcagtcacccaggctggagtgcagtggccagatgtcga
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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