VISDB - VIS Detail

Expression analysis of TCGA samples

Basic Information

VIS ID

TVIS10006767

Fusion event

HBV-SLC4A4 integration

Validated

Yes

Detection method

invPCR +Sequencing

Data source

Curated

Sample type

Tumor

Disease

Hepatocellular carcinoma (HCC)

Quality evaluation

Normal

Reported year

2016

PubMed ID

27453547

Virus Sequence

Virus name

HBV

Reference genome

V01460.1

Host Sequence

Chromosome

chr4

Cytoband

q13.3

Reference genome

GRCh38

Start

71522210 (Hg38)

End

71522210 (Hg38)

Location type

Intron

Target gene

SLC4A4

miRNAs that regulate target gene

hsa-mir-5585-3p ; hsa-mir-498 ; hsa-mir-4279 ; hsa-mir-6783-3p ; hsa-mir-1343-3p ; hsa-mir-23b-5p ; hsa-mir-23a-5p ; hsa-mir-6778-3p ; hsa-mir-1976 ; hsa-mir-3653-5p ; hsa-mir-6742-3p ; hsa-mir-6852-5p ; hsa-mir-939-3p ; hsa-mir-6747-3p ; hsa-mir-6727-3p ; hsa-mir-4722-3p ; hsa-mir-660-3p ; hsa-mir-6829-3p ; hsa-mir-6791-3p

Nearest miRNA

hsa-mir-12113/Upstream/5245282; hsa-mir-1243/Downstream/5051358;

Nearest TSS

ENST00000502981/Upstream/183157; ENST00000344413/Downstream/232268;

Nearest CpG islands

None/Target, chr4-CpG: 46/Upstream/334458, chr4-CpG: 30/Downstream/509637

Upstream sequence

AAATACCAGTACTCCATTGACAGTCTTTTTTGTATTCACCATCCTTTTTAAAGGGGTGTatcagtctgttatcccacactgtaactggtctgttctatca

Downstream sequence

gcctcgagtctttagtcagagtctttagtcaaattctttcagcatcaagacttccattaggaatatcacagcataatctgtgattttctgtggcaggtgg

Reference

Mason, W. S., et al. HBV DNA Integration and Clonal Hepatocyte Expansion in Chronic Hepatitis B Patients Considered Immune Tolerant. Gastroenterology,2016, 151(5): 986-998 e984.