Expression analysis of TCGA samples
Basic Information
VIS ID
TVIS10008818
Fusion event
HBV-TNRC6C integration
Validated
No
Detection method
NGS
Data source
Curated
Sample type
Disease
Hepatocellular carcinoma (HCC)
Quality evaluation
Normal
Reported year
2018
PubMed ID
Virus Sequence
Virus name
HBV
Reference genome
Region type
X protein|
Start
1777
Orient
+
Integrated sequence
AGCAATGTCAACGACCGACCTTGAGGCATACTTCAAAGACTGTTTGTTTAAAGACTGGGAGGAGTTGGGGGAGGAGATTAGGTTAAAGGTCTTTGTACTA| |GGAGGCTGTAGGCATAAATTGGTCTGCGCACCAGCACCATGCAACTTTTTCACCTCTGCCTAATCATCTCTTGTTCATGTCCTACTGTTCAAGCCTCCAA
Host Sequence
Chromosome
chr17
Cytoband
q25.3
Reference genome
Start
End
76010797/78014716 (Hg38)
Orient
+
Location type
Intronic
Target gene
miRNAs that regulate target gene
hsa-mir-30b-5p ; hsa-mir-4509 ; hsa-mir-4643 ; hsa-mir-95-5p ; hsa-mir-320a ; hsa-mir-331-5p ; hsa-mir-320b ; hsa-mir-320c ; hsa-mir-548m ; hsa-mir-320d ; hsa-mir-4429 ; hsa-mir-4666a-5p ; hsa-mir-125b-2-3p ; hsa-mir-380-3p ; hsa-mir-378a-5p ; hsa-mir-1200 ; hsa-mir-4666b ; hsa-mir-212-3p ; hsa-mir-132-3p ; hsa-mir-4709-5p ; hsa-mir-7159-5p ; hsa-mir-1273e ; hsa-mir-580-3p ; hsa-mir-539-5p ; hsa-mir-4635 ; hsa-mir-1264 ; hsa-mir-7152-5p ; hsa-mir-3074-5p ; hsa-mir-5700 ; hsa-mir-6512-5p ; hsa-mir-548ay-3p ; hsa-mir-548at-3p ; hsa-mir-548as-3p ; hsa-mir-548t-3p ; hsa-mir-548ap-3p ; hsa-mir-548aa ; hsa-mir-629-3p ; hsa-mir-519e-5p ; hsa-mir-515-5p ; hsa-mir-3925-3p ; hsa-mir-766-3p ; hsa-mir-1305 ; hsa-mir-4652-3p ; hsa-mir-421 ; hsa-mir-505-3p ; hsa-mir-8064 ; hsa-mir-3182 ; hsa-mir-216b-3p ; hsa-mir-603 ; hsa-mir-8485 ; hsa-mir-5010-3p ; hsa-mir-1238-3p ; hsa-mir-670-3p ; hsa-mir-6844 ; hsa-mir-6881-3p ; hsa-mir-6780a-3p ; hsa-mir-7111-3p ; hsa-mir-877-3p ; hsa-mir-4677-5p ; hsa-mir-22-5p ; hsa-mir-2116-5p ; hsa-mir-676-5p ; hsa-mir-4659b-3p ; hsa-mir-4659a-3p ; hsa-mir-6875-3p ; hsa-mir-511-5p ; hsa-mir-502-5p ; hsa-mir-6830-3p ; hsa-mir-1915-5p ; hsa-mir-6841-3p
Nearest miRNA
hsa-mir-10226/Upstream/617662; hsa-mir-1250/Downstream/1692460;
Nearest CpG islands
None/Target, chr17-CpG: 26/Upstream/54846, chr17-CpG: 31/Downstream/26188
Upstream sequence
TTCATGTTATCTAGTATGTGATGTATTGAGAGTGGCATTTGGTACCTTTTAGAGAGGTAACTGTAATATGCTAGAGTAGAAAATACCTCTGAACGGCATT
Downstream sequence
TCTCATTAGCAACAGACACTAAGTTAATGTAGTTTGTAGTTAATGAGTCTGTGCTTGTTTTGAGTTGGGCTCCAAATGTTGCCACGGTGATAGATCAGCC
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.