VISDB Viral Integration Site DataBase

VIS ID

TVIS20000062

Fusion event

HPV-PCDH9 integration

Validated

Yes

Detection method

PCR and Sanger sequencing

Data source

Curated

Sample type

Disease

Cervical carcinoma (CC)

Quality evaluation

Normal

Reported year

2016

PubMed ID

Virus name

HPV

Subtype

HPV16

Reference genome

Region type

E1

Start

2744

Integrated sequence

CACACCACTAAGTTGTTGCACAGAGACTCAGTGGACAGTGCTCCAATCCTCACTGCATTTAACAGCTCACACAAAGGACGGATTAACTGTAATAGTAACA| |CTACACCCATAGTACATTTAAAAGGTGATGCTAATACTTTAAAATGTTTAAGATATAGATTTAAAAAGCATTGTACATTGTATACTGCAGTGTCGTCTAC

Chromosome

chr13

Cytoband

q21.32

Reference genome

Start

End

67500034/66925902 (Hg38)

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/707578; hsa-mir-1267/Downstream/10772110;

Nearest TSS

Nearest CpG islands

None/Target, chr13-CpG: 551/Upstream/3081356, chr13-CpG: 92/Downstream/304474

Nearest cancer related gene

PCDH9(TSG, No orient, 0)

Upstream sequence

tATTATGATAATGATTATTACATTAATTTCCATAAATTTGTGATTGAAGAGTTCCCAGTTGCCTTTGGGAAAAAAAAAAAAAGCTTTAATGCGACCTAGT

Downstream sequence

GGCCTTTTAAAATATATTTGTGTCCTTCTGAAGATCAGAGGGGGCATGACTTCAGCAGGTCTTGGAGCATATGACATTGTTCATGTCCATTGTCTTCCTA