VISDB Viral Integration Site DataBase

VIS ID

TVIS20004275

Fusion event

HPV-CCDC39 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

Gene

E1

Start

1855

Integrated sequence

TTATGTGTGTCTCCAATGTGTATGATGATAGAGCCTCCAAAATTGCGTAGTACAGCAGCAGCATTATATTGGTATAAAACAGGTATATCAAATATTAGTG| |AAGTGTATGGAGACACGCCAGAATGGATACAAAGACAAACAGTATTACAACATAGTTTTAATGATTGTACATTTGAATTATCACAGATGGTACAATGGGC

Chromosome

chr3

Cytoband

q26.33

Reference genome

Start

End

180346143/180628355 (Hg38)

Location type

Intronic

Target gene

miRNAs that regulate target gene

hsa-mir-124-3p ; hsa-mir-3680-3p ; hsa-mir-557 ; hsa-mir-507 ; hsa-mir-450b-5p ; hsa-mir-758-3p ; hsa-mir-133b ; hsa-mir-133a-3p ; hsa-mir-5587-5p ; hsa-mir-19b-2-5p ; hsa-mir-19b-1-5p ; hsa-mir-19a-5p ; hsa-mir-8064 ; hsa-mir-6740-5p ; hsa-mir-1208 ; hsa-mir-4676-3p ; hsa-mir-452-5p ; hsa-mir-892c-3p ; hsa-mir-335-3p ; hsa-mir-421 ; hsa-mir-4742-3p ; hsa-mir-4709-5p

Nearest miRNA

hsa-let-7g/Upstream/4113204; hsa-mir-1224/Downstream/3258445;

Nearest TSS

Nearest CpG islands

None/Target, chr3-CpG: 148/Upstream/25750, chr3-CpG: 54/Downstream/50961

Junction sequence