VISDB - VIS Detail

Expression analysis of TCGA samples

Basic Information

VIS ID

TVIS10006377

Fusion event

HBV-SEC24A integration

Validated

Yes

Detection method

invPCR +Sequencing

Data source

Curated

Sample type

Tumor

Disease

Hepatocellular carcinoma (HCC)

Quality evaluation

Perfect

Reported year

2016

PubMed ID

27453547

Virus Sequence

Virus name

HBV

Reference genome

V01460.1

Start

1811

Integrated sequence

GCGACCCCGAGAAGGGTCGTCCGCAGGATTCAGCGCCGACGGGACGTAAACAAAGGACGTCCCGCGCAGGATCCAGTTGGCAGCACAGCCTAGCAGCCAT| |GGAAACGATGTATATTTGCGGGATAGGACAACAGAGTTATCAGTCCCGATAATGTTTGCTCCAGACCTGCTGCGAGCAAAACAAGCGGCTAGGAGTTCCG

Host Sequence

Chromosome

chr5

Cytoband

q31.1

Reference genome

GRCh38

Start

134702101 (Hg38)

End

134702101 (Hg38)

Location type

Intron

Fragile sites / regions

FRA5C

Target gene

SEC24A

miRNAs that regulate target gene

hsa-mir-16-5p ; hsa-mir-30a-5p ; hsa-mir-320a ; hsa-mir-125b-5p ; hsa-mir-92a-3p ; hsa-mir-377-5p ; hsa-mir-329-5p ; hsa-mir-655-5p ; hsa-mir-1294 ; hsa-mir-4316 ; hsa-mir-4464 ; hsa-mir-4524a-5p ; hsa-mir-4748 ; hsa-mir-5087 ; hsa-mir-4524b-5p ; hsa-mir-6086 ; hsa-mir-30c-5p ; hsa-mir-30d-5p ; hsa-mir-30b-5p ; hsa-mir-30e-5p ; hsa-mir-374a-5p ; hsa-let-7a-3p ; hsa-let-7b-3p ; hsa-let-7f-1-3p ; hsa-mir-98-3p ; hsa-mir-383-3p ; hsa-mir-381-3p ; hsa-mir-300 ; hsa-mir-218-5p ; hsa-mir-4666a-3p ; hsa-mir-758-3p ; hsa-mir-892c-5p ; hsa-mir-646 ; hsa-mir-424-5p ; hsa-mir-503-5p ; hsa-mir-6838-5p ; hsa-mir-15a-5p ; hsa-mir-15b-5p ; hsa-mir-195-5p ; hsa-mir-497-5p ; hsa-mir-6739-3p ; hsa-mir-375 ; hsa-mir-4677-5p ; hsa-mir-7156-5p ; hsa-mir-4273 ; hsa-mir-9-3p ; hsa-mir-22-5p ; hsa-mir-2116-5p ; hsa-mir-676-5p ; hsa-mir-4526 ; hsa-mir-3660 ; hsa-mir-888-3p ; hsa-mir-6507-5p ; hsa-mir-4429 ; hsa-mir-320d ; hsa-mir-320c ; hsa-mir-320b ; hsa-mir-186-5p ; hsa-mir-3133 ; hsa-mir-429 ; hsa-mir-200c-3p ; hsa-mir-200b-3p ; hsa-mir-5096 ; hsa-mir-4659b-3p ; hsa-mir-4659a-3p ; hsa-mir-664b-3p ; hsa-mir-579-3p ; hsa-mir-5696 ; hsa-mir-6794-3p ; hsa-mir-197-3p ; hsa-mir-6837-3p ; hsa-mir-6754-3p ; hsa-mir-412-3p ; hsa-mir-27b-3p ; hsa-mir-27a-3p

Nearest miRNA

hsa-mir-10397/Upstream/476249; hsa-mir-103a-1/Downstream/1100884;

Nearest TSS

ENST00000502646/Upstream/22390; ENST00000514518/Downstream/36400;

Nearest CpG islands

None/Target, chr5-CpG: 87/Upstream/52797, chr5-CpG: 48/Downstream/36292

Downstream sequence

TTATCACAATATCTTGAAAAC

Junction sequence

TAAATTGGTCTGCGCACCAGTTATCACAATATCTTGAAAAC

* Color: Human Sequence / Virus Sequence / Overlapped sequence / Unknown sequence

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.