VISDB Viral Integration Site DataBase

VIS ID

TVIS20004078

Fusion event

HPV-RUNX1 integration

Validated

No

Detection method

RNA-Seq

Data source

Curated

Sample type

Disease

Head and neck squamous cell carcinoma (HNSCC)

Quality evaluation

Normal

Reported year

2018

PubMed ID

Virus name

HPV

Subtype

HPV33

Reference genome

Not given

Gene

E4

Start

827

Chromosome

chr21

Cytoband

q22.12

Reference genome

Start

End

36470144/35097847 (Hg38)

Location type

Intron7

Target gene

miRNAs that regulate target gene

hsa-mir-27a-3p ; hsa-mir-17-5p ; hsa-mir-20a-5p ; hsa-mir-106a-5p ; hsa-mir-423-5p ; hsa-mir-675-5p ; hsa-mir-8485 ; hsa-mir-221-3p ; hsa-mir-7111-3p ; hsa-mir-4792 ; hsa-mir-6721-5p ; hsa-mir-6860 ; hsa-mir-612 ; hsa-mir-5189-5p ; hsa-mir-3187-5p ; hsa-mir-1285-3p ; hsa-mir-939-3p ; hsa-mir-6769b-3p ; hsa-mir-4723-3p ; hsa-mir-3183 ; hsa-mir-6791-5p ; hsa-mir-4292 ; hsa-mir-4308 ; hsa-mir-4762-5p ; hsa-mir-605-5p ; hsa-mir-551b-5p ; hsa-mir-4417 ; hsa-mir-4467 ; hsa-mir-6853-5p ; hsa-mir-8072 ; hsa-mir-4530 ; hsa-mir-3960 ; hsa-mir-922 ; hsa-mir-4789-3p ; hsa-mir-335-3p ; hsa-mir-5096 ; hsa-mir-377-3p ; hsa-mir-6885-3p ; hsa-mir-4446-5p ; hsa-mir-7152-5p ; hsa-mir-5006-3p ; hsa-mir-4755-5p ; hsa-mir-3180-5p ; hsa-mir-4639-5p ; hsa-mir-4497 ; hsa-mir-642a-5p ; hsa-mir-513a-5p ; hsa-mir-3160-5p ; hsa-mir-1266-3p ; hsa-mir-4667-3p ; hsa-mir-1470 ; hsa-mir-7157-5p ; hsa-mir-4310 ; hsa-mir-141-5p ; hsa-mir-2115-3p ; hsa-mir-1179 ; hsa-mir-27b-3p ; hsa-mir-128-3p ; hsa-mir-216a-3p ; hsa-mir-3681-3p ; hsa-mir-18a-5p ; hsa-mir-215-5p ; hsa-mir-9-5p ; hsa-mir-101-3p ; hsa-mir-144-5p ; hsa-mir-181a-5p ; hsa-mir-378a-3p

Nearest miRNA

hsa-let-7c/Upstream/1547119; hsa-mir-3197/Downstream/622868;

Nearest TSS

Nearest CpG islands

None/Target, chr21-CpG: 261/Upstream/70885, chr21-CpG: 42/Downstream/789046

Nearest cancer related gene

RUNX1(TSG, No orient, 0)

Upstream sequence

tgatcacacagctgtcagaagtggagctgggactccaacccagggaggacgtctacagagcctagttcacacatctctgttcttccatcctTAAACCTTG

Downstream sequence

TAGAATGCAGTGGAGGAGCAAGGCAAGCTGCGGGCCATGGGGATTCTTTATTCTGATTATCTGAAAAGACCAAAGAGTTTAGACTGCTCACTGGGCTTCC