VISDB - VIS Detail

Expression analysis of TCGA samples

Basic Information

VIS ID

TVIS20004647

Fusion event

HPV-PDE4D 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

HPV18

Reference genome

NC_001357.1

Gene

E6

Start

379

End

420

Integrated sequence

ACTAACTAACACTGGGTTATACAATTTATTAATAAGGTGCCT

Host Sequence

Chromosome

chr5

Cytoband

q11.2

Reference genome

GRCh37/hg19

Start

58795213/59499387 (Hg38)

End

58795246/59499420 (Hg38)

Location type

Intronic

Fragile sites / regions

FRA5H

Target gene

PDE4D

miRNAs that regulate target gene

hsa-mir-335-5p ; hsa-mir-340-5p ; hsa-mir-7-5p ; hsa-mir-103a-3p ; hsa-mir-19b-3p ; hsa-mir-18a-5p ; hsa-mir-16-5p ; hsa-mir-3148 ; hsa-mir-4668-5p ; hsa-mir-4457 ; hsa-mir-5590-3p ; hsa-mir-142-5p ; hsa-mir-6783-5p ; hsa-mir-6838-5p ; hsa-mir-497-5p ; hsa-mir-424-5p ; hsa-mir-195-5p ; hsa-mir-15b-5p ; hsa-mir-15a-5p ; hsa-mir-6835-3p ; hsa-mir-548z ; hsa-mir-548h-3p ; hsa-mir-548d-3p ; hsa-mir-548bb-3p ; hsa-mir-7158-3p ; hsa-mir-548ac ; hsa-mir-31-3p ; hsa-mir-302f ; hsa-mir-4760-3p ; hsa-mir-4282 ; hsa-mir-18b-5p ; hsa-mir-4735-3p ; hsa-mir-4439 ; hsa-mir-3136-5p ; hsa-mir-6857-3p ; hsa-mir-6855-3p ; hsa-mir-4513 ; hsa-mir-4502 ; hsa-mir-4682 ; hsa-mir-1324 ; hsa-mir-4422 ; hsa-mir-3611 ; hsa-mir-4325 ; hsa-mir-4266 ; hsa-mir-642b-3p ; hsa-mir-642a-3p ; hsa-mir-6080 ; hsa-mir-6888-5p ; hsa-mir-3120-3p ; hsa-mir-3646 ; hsa-mir-424-3p ; hsa-mir-199a-5p ; hsa-mir-139-5p

Nearest miRNA

hsa-mir-10397/Upstream/969278; hsa-mir-103a-1/Downstream/204186;

Nearest TSS

ENST00000502646/Upstream/68787; ENST00000502993/Downstream/86973;

Nearest CpG islands

None/Target, chr5-CpG: 87/Upstream/459333, chr5-CpG: 47/Downstream/393799

Upstream sequence

ACCTAGAGCTAGCAGAAAAAAAAGAAATAACTAACTAA

Target sequence

cctagagctagcagaaaaaaaagaaataactaa

Junction sequence

ACCTAGAGCTAGCAGAAAAAAAAGAAATAACTAACTAACACTGGGTTATACAATTTATTAATAAGGTGCC

* 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.