VISDB Viral Integration Site DataBase

VIS ID

TVIS20005073

Fusion event

HPV-RARA 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

chr17

Cytoband

q21.2

Reference genome

Start

End

38487281/40331029 (Hg38)

Location type

Intronic

Target gene

miRNAs that regulate target gene

hsa-mir-125a-5p ; hsa-mir-218-5p ; hsa-mir-615-3p ; hsa-mir-138-5p ; hsa-mir-6780a-5p ; hsa-mir-6779-5p ; hsa-mir-3689c ; hsa-mir-3689b-3p ; hsa-mir-3689a-3p ; hsa-mir-30b-3p ; hsa-mir-1273h-5p ; hsa-mir-519e-5p ; hsa-mir-515-5p ; hsa-mir-6778-5p ; hsa-mir-1233-5p ; hsa-mir-6780b-5p ; hsa-mir-4725-3p ; hsa-mir-4271 ; hsa-mir-6799-5p ; hsa-mir-5196-5p ; hsa-mir-7106-5p ; hsa-mir-4747-5p ; hsa-mir-6797-5p ; hsa-mir-1249-5p ; hsa-mir-6133 ; hsa-mir-6130 ; hsa-mir-6129 ; hsa-mir-6127 ; hsa-mir-4510 ; hsa-mir-4419a ; hsa-mir-605-3p ; hsa-mir-3925-3p ; hsa-mir-766-3p ; hsa-mir-194-3p ; hsa-mir-6783-5p ; hsa-mir-4756-5p ; hsa-mir-4739 ; hsa-mir-1321 ; hsa-mir-940 ; hsa-mir-6893-5p ; hsa-mir-3714 ; hsa-mir-6808-5p ; hsa-mir-27a-3p

Nearest miRNA

hsa-mir-1180/Upstream/115623; hsa-mir-10226/Downstream/1186135;

Nearest TSS

Nearest CpG islands

chr17-CpG: 23/Target, None/Upstream, None/Downstream

Nearby gene

CDC6 ; GJD3(+) ;

Nearest cancer related gene

RARA(OG, No orient, 0)

Upstream sequence

CATCTCACCAGAGCAGAAAAACAAGTTCAACTGGGCACTTTAATCTCCCCTCACTGGCAGGCCTGGTGTGAGCTGCTACCCCGGCGCCCCTCACCAGGGG

Downstream sequence

TAGGGTGGGGGCTCCAGGAGACTGAGATTAGCCTGCCCTCTTTGGACAGCAGCTCCAGGACAGGGCGGGTGGGCTGACCACCCAAACCCCATCTGGGCCC

Target sequence

GTAGGACCATGCACACCCCTTCCCAATTCTTTGGCCGCCTTTGACCCCGGCCTCTGCTTCTGATCTAGCCATTTCCTTCTCGCCAGTTCTGGCTTTCCCCATCCCTCCTCTCCCGTCGCTCACTGTAGTCCTGGGAGGTGGGAGCCTGGGAACAGTGGGGTGTCTGAAAGCTCAGAGCCCTCTGCACCCTCCAGCACCCTTCCTGCATTTCTCCTGAGGCAGTTCCCGTTCTCTAGATAAGAGTGGGGAGTAGGG