VISDB - VIS Detail

Expression analysis of TCGA samples

Basic Information

VIS ID

TVIS20003958

Fusion event

HPV-IL17RD integration

Validated

No

Detection method

RNA-Seq

Data source

Curated

Sample type

Tumor

Disease

Head and neck squamous cell carcinoma (HNSCC)

Quality evaluation

Normal

Reported year

2018

PubMed ID

28928286

Virus Sequence

Virus name

HPV

Subtype

HPV16

Reference genome

Not given

Gene

E7

Start

805

Host Sequence

Chromosome

chr3

Cytoband

p14.3

Reference genome

GRCh37/hg19

Start

57154167/57120139 (Hg38)

End

57154167/57120139 (Hg38)

Location type

Exon2

Target gene

IL17RD

miRNAs that regulate target gene

hsa-mir-335-5p ; hsa-mir-193b-3p ; hsa-mir-1976 ; hsa-mir-3653-5p ; hsa-mir-4279 ; hsa-mir-4722-3p ; hsa-mir-498 ; hsa-mir-6727-3p ; hsa-mir-6747-3p ; hsa-mir-6819-3p ; hsa-mir-6877-3p

Nearest miRNA

hsa-let-7g/Upstream/1267545; hsa-mir-12124/Downstream/3497666;

Nearest TSS

ENST00000440867/Upstream/40810; ENST00000468342/Downstream/22352;

Nearest CpG islands

None/Target, chr3-CpG: 148/Upstream/21760, chr3-CpG: 125/Downstream/44076

Nearest cancer related gene

IL17RD(TSG, No orient, 0)

Upstream sequence

tggccaacatggtgaaactccatctctactaaaaatacaaaaattagctgggcatggtggcatgcacctgtagtcccagctactcgggaggctgagacag

Downstream sequence

ACAGGTTCAGAAAATTCGTCAACCCCAAGACTGCAGAGTCCTTGATTAAGCATGGCTATGTAATCTCTAGATGACTCAAAGGGCTCCATTCTTCAGCAAT

Reference

Koneva, L. A., et al. HPV Integration in HNSCC Correlates with Survival Outcomes, Immune Response Signatures, and Candidate Drivers. Mol Cancer Res ,2018,16(1): 90-102.