VISDB Viral Integration Site DataBase

VIS ID

TVIS10011478

Fusion event

HBV-SHANK2 integration

Validated

No

Detection method

NGS

Data source

Curated

Sample type

Disease

Hepatocellular carcinoma (HCC)

Quality evaluation

Normal

Reported year

2018

PubMed ID

Virus name

HBV

Reference genome

Region type

X protein|precore/core protein|

Start

1827

Orient

-

Integrated sequence

AAGACTGGGAGGAGTTGGGGGAGGAGATTAGGTTAAAGGTCTTTGTACTAGGAGGCTGTAGGCATAAATTGGTCTGCGCACCAGCACCATGCAACTTTTT| |CACCTCTGCCTAATCATCTCTTGTTCATGTCCTACTGTTCAAGCCTCCAAGCTGTGCCTTGGGTGGCTTTGGGGCATGGACATCGACCCTTATAAAGAAT

Chromosome

chr11

Cytoband

q13.4

Reference genome

Start

End

70657436/70811331 (Hg38)

Orient

-

Location type

Intronic

Fragile sites / regions

Target gene

miRNAs that regulate target gene

hsa-mir-1307-3p ; hsa-mir-155-5p ; hsa-mir-4646-3p ; hsa-mir-4433b-5p ; hsa-mir-4433a-5p ; hsa-mir-4469 ; hsa-mir-4667-3p ; hsa-mir-1470 ; hsa-mir-6756-3p ; hsa-mir-3127-3p

Nearest miRNA

hsa-mir-10392/Upstream/527261; hsa-let-7a-2/Downstream/60939;

Nearest TSS

Nearest CpG islands

None/Target, chr11-CpG: 30/Upstream/93550, chr11-CpG: 34/Downstream/8992

Upstream sequence

GAGCAGGAGTCACAGGGTCTGTTCACAACTGTTATGTGTCTGACACAGCAGCTGCTTAAGTCCAGAACTTAGGAACCAAATGAGGAGTGCGTCTTCTCAG

Downstream sequence

GATTTCCACACCCAAAGAGCTCCTGCAAGGAACCCCACGGCCCCACTGTGCATCCTCAACAGCAGCCGGCAAGGGACACTGAGCCTGCCCTGCTTGAGAA