VISDB Viral Integration Site DataBase

VIS ID

TVIS20004310

Fusion event

HPV-TRPC4AP 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

L1

Start

6456

Integrated sequence

AACCATATGGCGACAGCTTATTTTTTTATTTACGAAGGGAACAAATGTTTGTTAGACATTTATTTAATAGGGCTGGTACTGTTGGTGAAAATGTACCAGA| |CGATTTATACATTAAAGGCTCTGGGTCTACTGCAAATTTAGCCAGTTCAAATTATTTTCCTACACCTAGTGGTTCTATGGTTACCTCTGATGCCCAAATA

Chromosome

chr20

Cytoband

q11.22

Reference genome

Start

End

33638717/35050914 (Hg38)

Location type

Intronic

Target gene

miRNAs that regulate target gene

hsa-mir-320b ; hsa-mir-324-5p ; hsa-mir-106b-5p ; hsa-mir-93-5p ; hsa-mir-4439 ; hsa-mir-3136-5p ; hsa-mir-4314 ; hsa-mir-6749-3p ; hsa-mir-6792-3p ; hsa-mir-4691-5p ; hsa-mir-365b-5p ; hsa-mir-365a-5p ; hsa-mir-8052 ; hsa-mir-3199 ; hsa-mir-4740-5p ; hsa-mir-6857-3p ; hsa-mir-6855-3p ; hsa-mir-4513 ; hsa-mir-2277-3p ; hsa-mir-6506-5p ; hsa-mir-619-5p ; hsa-mir-3192-5p ; hsa-mir-4646-5p ; hsa-mir-204-3p ; hsa-mir-4526 ; hsa-mir-3660 ; hsa-mir-330-5p ; hsa-mir-326 ; hsa-mir-4286 ; hsa-mir-6777-3p ; hsa-mir-141-5p ; hsa-mir-888-3p ; hsa-mir-514a-5p

Nearest miRNA

hsa-mir-103a-2/Upstream/60417; hsa-mir-1-1/Downstream/403040;

Nearest TSS

Nearest CpG islands

None/Target, chr20-CpG: 39/Upstream/53267, chr20-CpG: 86/Downstream/41338

Junction sequence