VISDB Viral Integration Site DataBase

VIS ID

TVIS20003817

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

2067

Integrated sequence

TACGTGACCATATAGACTATTGGAAACACATGCGCCTAGAATGTGCTATTTATTACAAGGCCAGAGAAATGGGATTTAAACATATTAACCACCAGGTGGT| |GCCAACACTGGCTGTATCAAAGAATAAAGCATTACAAGCAATTGAACTGCAACTAACGTTAGAAACAATATATAACTCACAATATAGTAATGAAAAGTGG

Chromosome

chr21

Cytoband

q11.2

Reference genome

Start

End

16427783/15055462 (Hg38)

Orient

-

Location type

Intron1

Fragile sites / regions

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-mir-10396a/Upstream/1331188; hsa-let-7c/Downstream/1483627;

Nearest TSS

Nearest CpG islands

None/Target, chr21-CpG: 261/Upstream/671697, chr21-CpG: 171/Downstream/8713

Upstream sequence

AAAGTAGAGCTGGCCTGTGAGTGTTCTGGTCAACTAAAGGTATCTGGCTCTCTTTGTCTGCAAATAAATAGCAAGTCTCCCTACTTCTTTTTAAATAAAA

Downstream sequence

AGTACTAGAATATTCAACAAATCCTAAGACTTTTATGAAGACCATGAGAAGAAAATAAGGTACTAGAACAAAAGTGATGCAGCCAGCCAATTCTCGTTTC

Target sequence

TTCCAAATGTACGTAACATGTAAAACAATGCCACTGCATGAACATGTACATAACTGTACTATTCTTTTTTTAAATTCTCAGCCTGGAAATTACATTTCA