VISDB - VIS Detail

Expression analysis of TCGA samples

Basic Information

VIS ID

TVIS10010305

Fusion event

HBV-THEM4 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

chr1

Cytoband

q21.3

Reference genome

GRCh37/hg19

Start

151852568/151880092 (Hg38)

End

151852568/151880092 (Hg38)

Orient

-

Location type

Intronic

Fragile sites / regions

FRA1F

Target gene

THEM4

miRNAs that regulate target gene

hsa-mir-30a-5p ; hsa-mir-16-5p ; hsa-mir-8057 ; hsa-mir-6749-3p ; hsa-mir-6792-3p ; hsa-mir-4691-5p ; hsa-mir-24-3p ; hsa-mir-4284 ; hsa-mir-4772-3p ; hsa-mir-1236-3p ; hsa-mir-1304-3p ; hsa-mir-877-3p ; hsa-mir-660-3p ; hsa-mir-5193 ; hsa-mir-6890-3p ; hsa-mir-5089-5p ; hsa-mir-5589-5p ; hsa-mir-4731-5p ; hsa-mir-6829-3p ; hsa-mir-6791-3p ; hsa-mir-6506-5p ; hsa-mir-619-5p ; hsa-mir-7107-5p ; hsa-mir-1234-3p ; hsa-mir-5009-3p ; hsa-mir-512-3p ; hsa-mir-520e ; hsa-mir-520d-3p ; hsa-mir-520c-3p ; hsa-mir-520b ; hsa-mir-520a-3p ; hsa-mir-373-3p ; hsa-mir-372-3p ; hsa-mir-302e ; hsa-mir-302d-3p ; hsa-mir-302c-3p ; hsa-mir-302b-3p ; hsa-mir-302a-3p ; hsa-mir-4796-3p ; hsa-mir-93-5p ; hsa-mir-526b-3p ; hsa-mir-519d-3p ; hsa-mir-20b-5p ; hsa-mir-20a-5p ; hsa-mir-17-5p ; hsa-mir-106b-5p ; hsa-mir-106a-5p ; hsa-mir-3609 ; hsa-mir-548ah-5p

Nearest miRNA

hsa-mir-101-1/Upstream/334201; hsa-mir-1182/Downstream/1809613;

Nearest TSS

ENST00000473358/Upstream/26395; ENST00000432386/Downstream/9658;

Nearest CpG islands

None/Target, chr1-CpG: 111/Upstream/40043, chr1-CpG: 66/Downstream/29195

Upstream sequence

ggagacagggtctcagtatgttgctcaggctgcagttcagtggctattcacaggagttatcatagtgcattgcagccttgaacccctggactaaagcaat

Downstream sequence

cctcctgcctcagcctcccaaatagctgggactatagatgtgcaccacctcacttggcTCTGATTTTTTttttttgtctgcttgacctatcaataattga

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.