CCDC88A _LIHC.png
Expression analysis of TCGA samples
Basic Information
VIS ID
TVIS10008519
Fusion event
HBV-CCDC88A 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
Polymerase|large S protein|middle S protein|
Start
40
Orient
-
Integrated sequence
AATTCCACAACCTTCCACCAAACTCTGCAAGATCCCAGAG| |TGAGAGGCCTGTATTTCCCTGCTGGTGGCTCCAGTTCAGGAACAGTAAACCCTGTTCTGACTACTGCCTCTCCCTTATCGTCAATCTTCTCGAGGATTGG
Host Sequence
Chromosome
chr2
Cytoband
p16.1
Reference genome
GRCh37/hg19
Start
55560692/55333556 (Hg38)
End
55560692/55333556 (Hg38)
Orient
-
Location type
Intronic
Fragile sites / regions
FRA2S
Target gene
CCDC88A
miRNAs that regulate target gene
hsa-mir-375 ; hsa-mir-4448 ; hsa-mir-8085 ; hsa-mir-4644 ; hsa-mir-6731-5p ; hsa-mir-4306 ; hsa-mir-185-5p ; hsa-mir-6133 ; hsa-mir-6130 ; hsa-mir-6129 ; hsa-mir-6127 ; hsa-mir-4510 ; hsa-mir-4419a ; hsa-mir-6760-5p ; hsa-mir-6873-5p ; hsa-mir-583 ; hsa-mir-4311 ; hsa-mir-101-5p
Nearest miRNA
hsa-mir-1301/Upstream/1484351; hsa-mir-10b/Downstream/649411;
Nearest TSS
ENST00000437798/Upstream/3388; ENST00000403007/Downstream/595;
Nearest CpG islands
None/Target, chr2-CpG: 135/Upstream/50972, chr2-CpG: 54/Downstream/85929
Upstream sequence
TGATTTGCATTCTCTGGCTTTGAGGTCAAAATTCATGgggctttggagtctgaaaaatctggatttgaatccagtaatccaactctgctatttattagct
Downstream sequence
gtgtgatcctaatttatttaatgtttctgaacctcagttttctcatctaaaaaatggatataatacttataaaggattagttgtaaagattatgtgcatg
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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