VISDB - VIS Detail

Expression analysis of TCGA samples

Basic Information

VIS ID

TVIS10016956

Fusion event

HBV-FAR2 integration

Validated

No

Detection method

Capture-NGS platform

Data source

Curated

Sample type

Tumor

Disease

Hepatocellular carcinoma (HCC)

Quality evaluation

Good

Reported year

2019

PubMed ID

30070724

Virus Sequence

Virus name

HBV

Subtype

C

Reference genome

NC_003977

Start

1598

End

1684

Integrated sequence

CTGCACGTCGCATGGAGACCACCGTGAACGCCCACCAAATATTGCCCAAGGTCTTACATAAGAGGACTCTTGGACTCTCAGCAATGT

Host Sequence

Chromosome

chr12

Cytoband

p11.22

Reference genome

GRCh37/hg19

Start

29326687/29173754 (Hg38)

End

29326781/29173848 (Hg38)

Location type

Intron

Target gene

FAR2

miRNAs that regulate target gene

hsa-mir-6715b-3p ; hsa-mir-6818-3p ; hsa-mir-593-3p ; hsa-mir-6895-3p ; hsa-mir-4766-5p ; hsa-mir-372-5p ; hsa-mir-371a-5p ; hsa-mir-616-5p ; hsa-mir-373-5p ; hsa-mir-371b-5p ; hsa-mir-935 ; hsa-mir-6715a-3p ; hsa-mir-1277-5p ; hsa-mir-3924 ; hsa-mir-190a-3p ; hsa-mir-4698 ; hsa-mir-5011-5p ; hsa-mir-8063

Nearest miRNA

hsa-mir-1244-3/Upstream/3299675; hsa-let-7i/Downstream/13149852;

Nearest TSS

ENST00000382841/Upstream/16763; ENST00000552137/Downstream/49817;

Nearest CpG islands

None/Target, chr12-CpG: 104/Upstream/23733, chr12-CpG: 30/Downstream/206665

Upstream sequence

ATGAGACCCAAAAAAATCTCTGTCTCTTCCAATGACCTATATTATATTGTAGTGACTGTAGATAAGCAATATAATTTTGTTTAGAATTTATAAGGAAACA

Downstream sequence

ctcctagaccacaaggaggactgaggaaggttggatttagtggcccttactaacacattctcaaaaacctgcacccttgcctgtcctcttagaccacaaa

Target sequence

acaccccccctacccaagaacccgcgacagtccctagaccctgctgatcagaatagttgcactcacctacgcagcagcagaaacactagttttc

Reference

Li, C. L., et al.Androgen Receptor Enhances Hepatic Telomerase Reverse Transcriptase Gene Transcription After Hepatitis B Virus Integration or Point Mutation in Promoter Region. Hepatology,2019, 69(2): 498-512.