VISDB Viral Integration Site DataBase

VIS ID

TVIS10020348

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

1183

End

2279

Orient

+

Integrated sequence

TTGCTGACGCAACCCCCACGGGTTGGGGCTTGGCCATAGGCCATCGGCGCATGCGTGGAACCTTTGTGGCTCCTCTGCCGATCCATACTGCGGAACTCCTAGCAGCTTGTTTTGCTCGCAGCCGGTCTGGAGCGAAACTTATCGGAACCGACAACTCAGTTGTCCTCTCTCGGAAATACACCTCCTTTCCATGGCTGCTAGGCTGTGCTGCCAACTGGATCCTGCGCGGGACGTCCTTTGTCTACGTCCCGTCGG

Chromosome

chr13

Cytoband

q21.32

Reference genome

Start

End

66930695/66356563 (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/137191; hsa-mir-1267/Downstream/11341449;

Nearest TSS

Nearest CpG islands

None/Target, chr13-CpG: 551/Upstream/2510969, chr13-CpG: 92/Downstream/873813

Nearest cancer related gene

PCDH9(TSG, No orient, 0)

Upstream sequence

aacatctcacagaagattgcttcagcctgatcctccacaggatgtttgcaatataagttaacacctcagagattgtcctggggcaaaggaaatgggcttc

Downstream sequence

GGTTTTTAAACGTCTGTCATTATATCAACAACATTAATGTAGCTTTTACACAAAAGGCAAGTGAAACAAAGTGCAAAAACAAAGATGATACAGTAGGACC

Target sequence

atagggctgacatgctgtctagtgttcttaagcactagaaggctctgatgtgccttaacagaaagagcacatgtgttagatcagctttgttcaggcatgagctatcgtactgttggccattgagtttaatttaatgaattaacaatatacattaaataaggcatctttaaacagaaacacacataaaacaaggttatgtattgattgtttgatgaaaataaagtgaccacaggctcacaggggcctaactttgta