VISDB Viral Integration Site DataBase

VIS ID

TVIS20004303

Fusion event

HPV-FRMPD4 integration

Validated

Yes

Detection method

WGS, RNA-seq, Whole-Exome sequencing, PCR

Data source

Curated

Sample type

Disease

Head and neck squamous cell carcinoma (HNSCC)

Quality evaluation

Perfect

Reported year

2014

PubMed ID

Virus name

HPV

Subtype

HPV16

Reference genome

Region type

LCR

Start

7360

Integrated sequence

TAATAAACACGTGTGTATGTGTTTTTAAATGCTTGTGTAACTATTGTGTCATGCAACATAAATAAACTTATTGTTTCAACACCTACTAATTGTGTTGTGG| |TTATTCATTGTATATAAACTATATTTGCTACATCCTGTTTTTGTTTTATATATACTATATTTTGTAGCGCCAGCGGCCATTTTGTAGCTTCAACCGAATT

Chromosome

chrX

Cytoband

p22.2

Reference genome

Start

End

12279942/12261823 (Hg38)

Location type

Intronic

Target gene

miRNAs that regulate target gene

hsa-mir-185-5p ; hsa-mir-6864-5p ; hsa-mir-519e-5p ; hsa-mir-515-5p ; hsa-mir-3179 ; hsa-mir-6763-3p ; hsa-mir-7515 ; hsa-mir-5695 ; hsa-mir-519d-5p ; hsa-mir-5587-3p ; hsa-mir-4707-5p ; hsa-mir-4279 ; hsa-mir-6749-3p ; hsa-mir-642a-5p ; hsa-mir-1268b ; hsa-mir-1268a ; hsa-mir-942-5p ; hsa-mir-4469 ; hsa-mir-3189-3p ; hsa-mir-212-5p ; hsa-mir-877-3p ; hsa-mir-2276-5p ; hsa-mir-6892-3p ; hsa-mir-483-3p

Nearest miRNA

hsa-mir-3690-1/Upstream/943137; hsa-let-7f-2/Downstream/1328469;

Nearest TSS

Nearest CpG islands

None/Target, chrX-CpG: 62/Upstream/122668, chrX-CpG: 27/Downstream/321540

Junction sequence