VISDB - VIS Detail

Expression analysis of TCGA samples

Basic Information

VIS ID

TVIS20000022

Fusion event

HPV-RFX3 integration

Validated

Yes

Detection method

PCR Ion Torrent Sequencing

Data source

Curated

Sample type

Tumor

Disease

Cervical carcinoma (CC)

Quality evaluation

Normal

Reported year

2016

PubMed ID

26660085

Virus Sequence

Virus name

HPV

Subtype

HPV16

Reference genome

NC_001526.4

Host Sequence

Chromosome

chr9

Cytoband

p24.2

Reference genome

NCBI36/hg18

Start

3364982/3374982 (Hg38)

End

3364982/3374982 (Hg38)

Location type

Intronic

Target gene

RFX3

miRNAs that regulate target gene

hsa-mir-335-5p ; hsa-mir-148b-3p ; hsa-mir-128-3p ; hsa-mir-615-3p ; hsa-mir-342-3p ; hsa-mir-4698 ; hsa-mir-892c-5p ; hsa-mir-4428 ; hsa-mir-3646 ; hsa-mir-3662 ; hsa-mir-1264 ; hsa-mir-4668-5p ; hsa-mir-6738-3p ; hsa-mir-544a ; hsa-mir-3977 ; hsa-mir-6071 ; hsa-mir-6828-3p ; hsa-mir-222-5p

Nearest miRNA

hsa-mir-1302-9/Upstream/3344701; hsa-let-7a-1/Downstream/1475315;

Nearest TSS

ENST00000422679/Upstream/28218; ENST00000430387/Downstream/20606;

Nearest CpG islands

None/Target, chr9-CpG: 64/Upstream/193115, chr9-CpG: 89/Downstream/151039

Upstream sequence

GAGTAGATAACATTTAAGACTTCTTCCAGCTCCACAGTCTTCAAATTAGCATTAACAACAGTTACGTAATTTATCATTGTCATGATACAAGGTTCATGAA

Downstream sequence

CAAAATTAGAACAAAAAATTATTTATCCCATAAATATTATCCATACTATTTGCAGTATGTACATTATAAACATTAATCTCTATGATCCAACAAATGAGCC

Reference

Bodelon, C., et al. Chromosomal copy number alterations and HPV integration in cervical precancer and invasive cancer. Carcinogenesis.2016, 37(2): 188-196.