VISDB Viral Integration Site DataBase

VIS ID

TVIS20003816

Fusion event

HPV-TRMO integration

Validated

Yes

Detection method

APOT and sequencing

Data source

Curated

Sample type

Disease

Head and neck squamous cell carcinoma (HNSCC)

Quality evaluation

Normal

Reported year

2015

PubMed ID

Virus name

HPV

Subtype

HPV16

Reference genome

Gene

E1

Start

2099

Integrated sequence

CGCCTAGAATGTGCTATTTATTACAAGGCCAGAGAAATGGGATTTAAACATATTAACCACCAGGTGGTGCCAACACTGGCTGTATCAAAGAATAAAGCAT| |TACAAGCAATTGAACTGCAACTAACGTTAGAAACAATATATAACTCACAATATAGTAATGAAAAGTGGACATTACAAGACGTTAGCCTTGAAGTGTATTT

Chromosome

chr9

Cytoband

q22.33

Reference genome

Start

End

100676842/97914560 (Hg38)

Orient

-

Location type

Intron2

Target gene

miRNAs that regulate target gene

hsa-mir-5096 ; hsa-mir-3187-3p ; hsa-mir-4435 ; hsa-mir-588 ; hsa-mir-4701-5p ; hsa-mir-548s ; hsa-mir-197-3p ; hsa-mir-4755-3p ; hsa-mir-98-5p ; hsa-mir-4500 ; hsa-mir-4458 ; hsa-let-7i-5p ; hsa-let-7g-5p ; hsa-let-7f-5p ; hsa-let-7e-5p ; hsa-let-7d-5p ; hsa-let-7c-5p ; hsa-let-7b-5p ; hsa-let-7a-5p ; hsa-mir-4716-5p ; hsa-mir-4781-3p ; hsa-mir-296-3p ; hsa-mir-4478 ; hsa-mir-4419b ; hsa-mir-3929 ; hsa-mir-562 ; hsa-mir-6818-5p ; hsa-mir-190a-3p ; hsa-mir-6820-3p ; hsa-mir-3164 ; hsa-mir-3118 ; hsa-mir-134-5p ; hsa-mir-16-1-3p ; hsa-mir-511-3p ; hsa-mir-5011-5p ; hsa-mir-5580-3p ; hsa-mir-1277-5p ; hsa-mir-6867-5p ; hsa-mir-7703 ; hsa-mir-6720-5p ; hsa-mir-6512-3p ; hsa-mir-6729-5p ; hsa-mir-4649-5p ; hsa-mir-661 ; hsa-mir-4696 ; hsa-mir-4486 ; hsa-mir-766-3p ; hsa-mir-939-3p ; hsa-mir-6849-3p ; hsa-mir-451b ; hsa-mir-508-5p ; hsa-mir-4432 ; hsa-mir-1276 ; hsa-mir-1273h-5p ; hsa-mir-149-3p ; hsa-mir-1827 ; hsa-mir-1910-3p ; hsa-mir-30b-3p ; hsa-mir-3192-5p ; hsa-mir-3612 ; hsa-mir-3689a-3p ; hsa-mir-3689b-3p ; hsa-mir-3689c ; hsa-mir-4537 ; hsa-mir-455-3p ; hsa-mir-4728-5p ; hsa-mir-4756-3p ; hsa-mir-490-3p ; hsa-mir-5186 ; hsa-mir-650 ; hsa-mir-6511a-5p ; hsa-mir-6516-5p ; hsa-mir-6779-5p ; hsa-mir-6780a-5p ; hsa-mir-6785-5p ; hsa-mir-6799-5p ; hsa-mir-6883-5p ; hsa-mir-7106-5p ; hsa-mir-7851-3p

Nearest miRNA

hsa-let-7a-1/Upstream/550879; hsa-mir-12126/Downstream/314589;

Nearest TSS

Nearest CpG islands

None/Target, chr9-CpG: 64/Upstream/56650, chr9-CpG: 53/Downstream/7656

Upstream sequence

ATCAGGCAAAAATGTAAAAAACTGATAACATATTGTGTTGGGAAGGGTGTAAGAAAAAGGTCATTTGCATATATTATTGAAGTATACATTGGTTAATTTT

Downstream sequence

GGCCAAGAATGTGTCTAAGGGGGTTTGTCACAGTTATTATAACAACAACATAGCCCTCCATTAACAAGAGTGTGTATATTACAAAATATACATCTATATT

Target sequence

AGAGGATAATTTGGAAGTAGTTCCCCAAAATTCTAAATATGCTTACCTTCTAACCCAATATATCCACTTCTGATATCCTGTTCATAAAAATACATAAGT