VISDB Viral Integration Site DataBase

VIS ID

TVIS10008018

Fusion event

HBV-CSMD1 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

precore/core protein|Core and e antigen|

Start

2170

Orient

+

Integrated sequence

CAAGCAATTCTTTGCTGGGGGGAACTAATGACTCTAGCTACCTGGGTGGGTGTTAATTTGGAAGATCCAGCGTCTAGAGACCTAGTAGTCAGTTATGTCA| |ACACTAATATGGGCCTAAAGTTCAGGCAACTCTTGTGGTTTCACATTTCTTGTCTCACTTTTGGAAGAGAAACAGTTATAGAGTATTTGGTGTCTTTCGG

Chromosome

chr8

Cytoband

p23.2

Reference genome

Start

End

3420958/3563436 (Hg38)

Orient

+

Location type

Intronic

Target gene

miRNAs that regulate target gene

hsa-mir-297 ; hsa-mir-3924 ; hsa-mir-190a-3p ; hsa-mir-4789-5p ; hsa-mir-567 ; hsa-mir-5011-5p ; hsa-mir-4704-5p ; hsa-mir-5583-3p ; hsa-mir-4517 ; hsa-mir-1277-5p ; hsa-mir-338-5p ; hsa-let-7c-3p ; hsa-mir-10b-5p

Nearest miRNA

hsa-mir-3674/Upstream/1486796; hsa-mir-10400/Downstream/3058688;

Nearest TSS

Nearest CpG islands

None/Target, chr8-CpG: 109/Upstream/541010, chr8-CpG: 256/Downstream/1428010

Nearest cancer related gene

CSMD1(TSG, No orient, 0)

Upstream sequence

cactgcactccagcctgggcagcctgggcgacagagtgagactctgtctcaattaaaagaaaaaaaaaaaagaaaagaaaagaaaaagaaaagaaaaCAT

Downstream sequence

AAAGGTaaaaaaaaaaaaaaaaaaaaaaGGACCACATCTAAGACCTGTAAAACTAACTGAGCTCCAAAGAAAATAGGTATTTACACCTCCCTGTATCTTA