VISDB Viral Integration Site DataBase

VIS ID

TVIS20004265

Fusion event

HPV-CD274 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

6757

Integrated sequence

AAATATGTCATTATGTGCTGCCATATCTACTTCAGAAACTACATATAAAAATACTAACTTTAAGGAGTACCTACGACATGGGGAAGAATATGATTTACAG| |TTTATTTTTCAACTGTGCAAAATAACCTTAACTGCAGACGTTATGACATACATACATTCTATGAATTCCACTATTTTGGAGGACTGGAATTTTGGTCTAC

Chromosome

chr9

Cytoband

p24.1

Reference genome

Start

End

5464509/5464509 (Hg38)

Location type

Intronic

Target gene

miRNAs that regulate target gene

hsa-mir-513a-5p ; hsa-mir-103a-3p ; hsa-mir-16-5p ; hsa-mir-570-3p ; hsa-mir-651-3p ; hsa-mir-3978 ; hsa-mir-593-3p ; hsa-mir-885-3p ; hsa-mir-380-5p ; hsa-mir-124-3p ; hsa-mir-601 ; hsa-mir-708-5p ; hsa-mir-34b-5p ; hsa-mir-665 ; hsa-mir-940 ; hsa-mir-326 ; hsa-mir-363-5p ; hsa-mir-214-3p ; hsa-mir-29c-3p ; hsa-mir-3977 ; hsa-mir-5706 ; hsa-mir-4782-5p ; hsa-mir-516b-5p ; hsa-mir-1299 ; hsa-mir-103a-2-5p ; hsa-mir-4790-3p ; hsa-mir-6128 ; hsa-mir-875-3p ; hsa-mir-4496 ; hsa-mir-138-5p ; hsa-mir-324-5p ; hsa-mir-338-5p ; hsa-mir-34a-3p ; hsa-mir-152-5p ; hsa-mir-200b-3p ; hsa-mir-152-3p ; hsa-mir-1273a ; hsa-mir-1273c ; hsa-mir-15a-5p ; hsa-mir-15b-5p ; hsa-mir-194-5p ; hsa-mir-195-5p ; hsa-mir-424-5p ; hsa-mir-4503 ; hsa-mir-497-5p ; hsa-mir-6792-5p ; hsa-mir-6838-5p

Nearest miRNA

hsa-mir-101-2/Upstream/614134; hsa-let-7a-1/Downstream/543317;

Nearest TSS

Nearest CpG islands

None/Target, chr9-CpG: 64/Upstream/13880, chr9-CpG: 107/Downstream/164061

Junction sequence