VISDB - VIS Detail

Expression analysis of TCGA samples

Basic Information

VIS ID

TVIS20004080

Fusion event

HPV-SEMA3E 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

754

Host Sequence

Chromosome

chr7

Cytoband

q21.11

Reference genome

GRCh37/hg19

Start

83082449/83453133 (Hg38)

End

83082449/83453133 (Hg38)

Location type

Intron4

Target gene

SEMA3E

miRNAs that regulate target gene

hsa-mir-615-3p ; hsa-mir-6878-3p ; hsa-mir-6741-3p ; hsa-mir-642a-5p ; hsa-mir-6830-3p ; hsa-mir-3124-3p ; hsa-mir-4778-3p ; hsa-mir-877-3p ; hsa-mir-2276-5p ; hsa-mir-6892-3p ; hsa-mir-4667-3p ; hsa-mir-1470 ; hsa-mir-6809-3p ; hsa-mir-6833-3p ; hsa-mir-4768-5p ; hsa-mir-6873-3p ; hsa-mir-6867-3p ; hsa-mir-6817-3p ; hsa-mir-7110-3p ; hsa-mir-6845-3p ; hsa-mir-4685-3p ; hsa-mir-4287 ; hsa-mir-7113-3p ; hsa-mir-4469 ; hsa-mir-4284 ; hsa-mir-2276-3p ; hsa-mir-4638-5p ; hsa-mir-1307-3p ; hsa-mir-1304-3p ; hsa-mir-4532 ; hsa-mir-1247-3p ; hsa-mir-6890-3p ; hsa-mir-4753-3p ; hsa-mir-222-5p ; hsa-mir-1236-3p ; hsa-mir-6515-3p ; hsa-mir-122-3p ; hsa-mir-6722-5p ; hsa-mir-1288-3p ; hsa-mir-6499-3p ; hsa-mir-17-3p ; hsa-mir-5693 ; hsa-mir-509-5p ; hsa-mir-509-3-5p ; hsa-mir-4418 ; hsa-mir-1250-3p ; hsa-mir-129-5p ; hsa-mir-153-5p ; hsa-mir-3672 ; hsa-mir-4294 ; hsa-mir-4743-5p ; hsa-mir-4754 ; hsa-mir-4760-3p ; hsa-mir-5696 ; hsa-mir-579-3p ; hsa-mir-664a-3p ; hsa-mir-664b-3p ; hsa-mir-6812-3p ; hsa-mir-6864-3p ; hsa-mir-8055

Nearest miRNA

hsa-mir-10525/Upstream/7537864; hsa-mir-10399/Downstream/8750882;

Nearest TSS

ENST00000635602/Upstream/97979; ENST00000450977/Downstream/9027;

Nearest CpG islands

None/Target, chr7-CpG: 39/Upstream/290037, chr7-CpG: 30/Downstream/296436

Upstream sequence

AGGATGCCCACCCTAAAAGTGAAATCTGCTGGCACTCATGATTTAGACAGTACATATCCCACGGAGGGTATGTTTTAAAAAACAGGCATGATGAAGTAAA

Downstream sequence

tctcctgtctcagcctccagagtagctgggattacaggggcccaccaccacgcctggctaatttttttgtattcctagtagagacggggtttcaccacat

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.