VISDB - VIS Detail

Expression analysis of TCGA samples

Basic Information

VIS ID

TVIS20004597

Fusion event

HPV-TP63 integration

Validated

Yes

Detection method

FISH, WGS, RNA-seq, qPCR

Data source

Curated

Sample type

Tumor

Disease

Cervical carcinoma (CC)

Quality evaluation

Perfect

Reported year

2014

PubMed ID

24201445

Virus Sequence

Virus name

HPV

Subtype

HPV16

Reference genome

NC_001526.2

Gene

E2

Start

3249

End

3265

Integrated sequence

ACATATTTTGTGCAGTT

Host Sequence

Chromosome

chr3

Cytoband

q28

Reference genome

GRCh37/hg19

Start

189596834/189879025 (Hg38)

End

189596814/189879045 (Hg38)

Location type

Intronic

Target gene

TP63

miRNAs that regulate target gene

hsa-mir-203a-3p ; hsa-mir-92a-3p ; hsa-mir-21-5p ; hsa-mir-124-3p ; hsa-mir-301b-3p ; hsa-mir-129-5p ; hsa-mir-6885-3p ; hsa-mir-4477b ; hsa-mir-1178-3p ; hsa-mir-6891-5p ; hsa-mir-3173-3p ; hsa-mir-4428

Nearest miRNA

hsa-let-7g/Upstream/49016; hsa-mir-3137/Downstream/5255461;

Nearest TSS

ENST00000440867/Upstream/89224; ENST00000412203/Downstream/85076;

Nearest CpG islands

None/Target, chr3-CpG: 148/Upstream/931262, chr3-CpG: 99/Downstream/241246

Nearest cancer related gene

TP63(TSG, No orient, 0)

Upstream sequence

AGTAATTTAATCTATCTGAGT

Target sequence

ctcagatagattaaattact

Junction sequence

AGTAATTTAATCTATCTGAGTAATACAAACATATTTTGTGCAGT

* Color: Human Sequence / Virus Sequence / Overlapped sequence / Unknown sequence

Reference

Akagi, K., et al.Genome-wide analysis of HPV integration in human cancers reveals recurrent, focal genomic instability. Genome Res ,2014,24(2): 185-199.