VISDB Viral Integration Site DataBase

VIS ID

TVIS10020246

Fusion event

HBV-PCDH9 integration

Validated

No

Detection method

VirusScan

Data source

Curated

Sample type

Disease

Hepatocellular carcinoma (HCC)

Quality evaluation

Good

Reported year

2016

PubMed ID

Virus name

HBV

Reference genome

Start

1176

End

2272

Orient

+

Integrated sequence

CAAGTGTTTGCTGACGCAACCCCCACGGGTTGGGGCTTGGCCATAGGCCATCGGCGCATGCGTGGAACCTTTGTGGCTCCTCTGCCGATCCATACTGCGGAACTCCTAGCAGCTTGTTTTGCTCGCAGCCGGTCTGGAGCGAAACTTATCGGAACCGACAACTCAGTTGTCCTCTCTCGGAAATACACCTCCTTTCCATGGCTGCTAGGCTGTGCTGCCAACTGGATCCTGCGCGGGACGTCCTTTGTCTACGTC

Chromosome

chr13

Cytoband

q21.32

Reference genome

Start

End

67252060/66677928 (Hg38)

Orient

+

Location type

Intronic

Fragile sites / regions

Target gene

miRNAs that regulate target gene

hsa-mir-155-5p ; hsa-mir-188-5p ; hsa-mir-127-5p ; hsa-mir-4635 ; hsa-mir-7843-3p ; hsa-mir-4735-3p ; hsa-mir-1264 ; hsa-mir-18b-5p ; hsa-mir-18a-5p ; hsa-mir-570-5p ; hsa-mir-548ba ; hsa-mir-548ai ; hsa-mir-548ag ; hsa-mir-548m

Nearest miRNA

hsa-mir-1297/Upstream/458556; hsa-mir-1267/Downstream/11020084;

Nearest TSS

Nearest CpG islands

None/Target, chr13-CpG: 551/Upstream/2832334, chr13-CpG: 92/Downstream/552448

Nearest cancer related gene

PCDH9(TSG, No orient, 0)

Upstream sequence

CCTCCCTTACTGAATTCCACAGCCTTCATGCTTATATTGGGCCAGACATTTAGCACACAAAGAGAATGGATGGATGCTTCCAGTATTTTTTTATTAATGC

Downstream sequence

GTTGGTTTCCCTTCAAAATACTTGCTTTGCACATAACTGCTTGTTATAAAAAACAATTTCAGCTTTACTTAAAAATCAGAAAGAGTAATTTTCCTTTTTA

Target sequence

TGCAATTAGCAAAAACAAAAGAATTAATGTTTGTTTTCCtttatattataaaattttaaatatCCATTTACATGTCAATATTGATTCATTTTCCAACTATTCAAAGTCGGTATGCGGATTAAAAGTTTTTTTAGATCACACCGAAGAAGATACAGATAGTGACACAGGAATGTCATGAAGGTTAATGGATTGACCATGGTTATAAAATCATTAAAGGGTGTGTAGCCATCAGAGTACCTGTCATCCTAACTTCTT