VISDB Viral Integration Site DataBase

VIS ID

TVIS10006888

Fusion event

HBV-GATM integration

Validated

Yes

Detection method

Alu PCR and sequencing

Data source

Curated

Sample type

Disease

Hepatocellular carcinoma (HCC)

Quality evaluation

Normal

Reported year

2015

PubMed ID

Virus name

HBV

Subtype

C2

Reference genome

Region type

Polymerase

Start

757

Integrated sequence

CCGTTTCTCCTGGCTCAGTTTACTAGTGCCATTTGTTCAGTGGTTCGTAGGGCTTTCCCCCACTGTTTGGCTTTCAGTTATATGGATGATGTGGTATTGG| |GGGCCAAGTCTGTACAACATCTTGAGTCCCTTTTTACCTCTATTACCAATTTTCTTTTGTCTTTGGGTATACATTTGAACCCTAATAAAACCAAACGTTG

Chromosome

chr15

Cytoband

q21.1

Reference genome

Start

End

45663260/45371062 (Hg38)

Location type

Intronic

Target gene

miRNAs that regulate target gene

hsa-mir-155-5p ; hsa-mir-215-5p ; hsa-mir-192-5p ; hsa-mir-6809-3p ; hsa-mir-6833-3p ; hsa-mir-4768-5p ; hsa-mir-4263 ; hsa-mir-297 ; hsa-mir-6873-3p ; hsa-mir-6830-3p ; hsa-mir-567 ; hsa-mir-6845-3p ; hsa-mir-1264 ; hsa-mir-3184-3p ; hsa-let-7a-5p ; hsa-let-7b-5p ; hsa-let-7c-5p ; hsa-let-7d-5p ; hsa-let-7e-5p ; hsa-let-7f-5p ; hsa-let-7g-5p ; hsa-let-7i-5p ; hsa-mir-126-5p ; hsa-mir-3677-5p ; hsa-mir-3926 ; hsa-mir-3927-3p ; hsa-mir-4257 ; hsa-mir-4458 ; hsa-mir-4460 ; hsa-mir-4480 ; hsa-mir-4500 ; hsa-mir-4727-3p ; hsa-mir-548ac ; hsa-mir-548ae-3p ; hsa-mir-548ah-3p ; hsa-mir-548aj-3p ; hsa-mir-548am-3p ; hsa-mir-548aq-3p ; hsa-mir-548bb-3p ; hsa-mir-548d-3p ; hsa-mir-548h-3p ; hsa-mir-548j-3p ; hsa-mir-548s ; hsa-mir-548x-3p ; hsa-mir-548z ; hsa-mir-6831-5p ; hsa-mir-8069 ; hsa-mir-944 ; hsa-mir-98-5p

Nearest miRNA

hsa-mir-10393/Upstream/653169; hsa-mir-11181/Downstream/61988;

Nearest TSS

Nearest CpG islands

None/Target, chr15-CpG: 55/Upstream/172008, chr15-CpG: 114/Downstream/6710

Upstream sequence

cagggtttcaccatgttggccaggctggtctcaatctcctgacctcgtgatccacccgcgtcggccccccaaagggctgggattataggtgtgagccacc

Downstream sequence

atgcccggccaaaatattggttttcaaaaatgtaaaaatctagacagattctgcattcagattgttttccaaatgtctaagttcttagtcaatttctcaa