VISDB Viral Integration Site DataBase

VIS ID

TVIS20005083

Fusion event

HPV-PTPRT integration

Validated

Yes

Detection method

RNA-Seq+RT-PCR

Data source

Curated

Sample type

Disease

Squamous-cell carcinoma (SCC)

Quality evaluation

Good

Reported year

2014

PubMed ID

Virus name

HPV

Subtype

HPV16

Reference genome

Chromosome

chr20

Cytoband

q12

Reference genome

Start

End

41658674/43030034 (Hg38)

Location type

Intronic

Target gene

miRNAs that regulate target gene

hsa-mir-335-5p ; hsa-mir-331-3p ; hsa-mir-10b-5p ; hsa-mir-10a-5p ; hsa-mir-16-5p ; hsa-mir-3928-3p ; hsa-mir-215-5p ; hsa-mir-3149 ; hsa-mir-630 ; hsa-mir-29a-5p ; hsa-mir-186-3p ; hsa-mir-664a-3p ; hsa-mir-5096 ; hsa-mir-197-3p ; hsa-mir-103a-2-5p ; hsa-mir-583 ; hsa-mir-1276 ; hsa-mir-4311 ; hsa-mir-6809-3p ; hsa-mir-5006-3p ; hsa-mir-4755-5p ; hsa-mir-4753-3p ; hsa-mir-211-5p ; hsa-mir-204-5p ; hsa-mir-623 ; hsa-mir-6832-3p ; hsa-mir-515-3p ; hsa-mir-5581-5p ; hsa-mir-7702 ; hsa-mir-4297 ; hsa-mir-6747-3p ; hsa-mir-4524b-3p ; hsa-mir-3909 ; hsa-mir-4494 ; hsa-mir-4633-3p ; hsa-mir-4738-3p ; hsa-mir-4766-3p ; hsa-mir-4773 ; hsa-mir-499b-5p ; hsa-mir-6500-5p ; hsa-mir-6736-3p ; hsa-mir-6852-3p ; hsa-mir-6874-5p

Nearest miRNA

hsa-mir-103a-2/Upstream/1801493; hsa-mir-1-1/Downstream/1378086;

Nearest TSS

Nearest CpG islands

None/Target, chr20-CpG: 39/Upstream/971186, chr20-CpG: 173/Downstream/158801

Nearby gene

CHD6 ; SRSF6(+) ;

Nearest cancer related gene

PTPRT(TSG, No orient, 0)

Upstream sequence

ccagagcttttagaagcggggcacactgctctttcaaaggaggagggaggcagagggctgatggatcagtgaattttcagctgacaacacgccttaagac

Downstream sequence

cagaggttatttattattgaagcataatctagcctatcctaactaaAATATCTTCTTCCTTTTTCTCTTTTTTTCTTCCACTAATTAAGCACCTACTAAA