VISDB - VIS Detail

Expression analysis of TCGA samples

Basic Information

VIS ID

TVIS20000130

Fusion event

HPV-TBC1D24 integration

Validated

Yes

Detection method

PCR and Sanger sequencing

Data source

Curated

Sample type

Tumor

Disease

Cervical carcinoma (CC)

Quality evaluation

Normal

Reported year

2016

PubMed ID

26735580

Virus Sequence

Virus name

HPV

Subtype

HPV18

Reference genome

NC_001526.2

Region type

E2

Start

2918

Integrated sequence

ATGTGTGTCAGGACAAAATAC TAACACATTATGAAAATGATAGTACAGACCTACGTGACCATATAGACTATTGGAAACACATGCGCCTAGA ATGTGCT| |ATTTATTACAAGGCCAGAGAAATGGGATTTAAACATATTAACCACCAAGTGGTGCCAACACTG GCTGTATCAAAGAATAAAGCATTACAAGCAATTGAA

Host Sequence

Chromosome

chr16

Cytoband

p13.3

Reference genome

GRCh37/hg19

Start

2539287/2489286 (Hg38)

End

2539287/2489286 (Hg38)

Location type

Intronic

Target gene

TBC1D24

miRNAs that regulate target gene

hsa-mir-1273e ; hsa-mir-6516-5p ; hsa-mir-455-3p ; hsa-mir-6807-5p ; hsa-mir-25-5p ; hsa-mir-658 ; hsa-mir-6499-3p ; hsa-mir-6086 ; hsa-mir-377-5p ; hsa-mir-6087 ; hsa-mir-6840-3p ; hsa-mir-665 ; hsa-mir-4459 ; hsa-mir-4695-5p ; hsa-mir-5694 ; hsa-mir-6736-5p ; hsa-mir-4701-3p ; hsa-mir-1262 ; hsa-mir-7703 ; hsa-mir-6720-5p ; hsa-mir-6512-3p ; hsa-mir-661 ; hsa-mir-4252 ; hsa-mir-4522 ; hsa-mir-6776-5p ; hsa-mir-4793-3p ; hsa-mir-766-3p ; hsa-mir-6742-3p ; hsa-mir-6849-3p ; hsa-mir-1273g-3p ; hsa-mir-3664-5p ; hsa-mir-508-5p ; hsa-mir-1228-3p ; hsa-mir-188-3p ; hsa-mir-532-3p ; hsa-mir-6778-3p ; hsa-mir-7112-5p ; hsa-mir-128-3p ; hsa-mir-216a-3p ; hsa-mir-2682-3p ; hsa-mir-3664-3p ; hsa-mir-3681-3p ; hsa-mir-3929 ; hsa-mir-4419b ; hsa-mir-4478 ; hsa-mir-4497 ; hsa-mir-4649-3p ; hsa-mir-4722-5p ; hsa-mir-485-5p ; hsa-mir-6732-3p ; hsa-mir-6747-3p ; hsa-mir-6752-3p ; hsa-mir-6781-3p ; hsa-mir-6808-5p ; hsa-mir-6884-5p ; hsa-mir-6893-5p ; hsa-mir-7160-5p ; hsa-mir-940

Nearest miRNA

hsa-mir-1225/Upstream/25248; hsa-mir-11401/Downstream/42636;

Nearest TSS

ENST00000527434/Upstream/6249; ENST00000627285/Downstream/4311;

Nearest CpG islands

None/Target, chr16-CpG: 29/Upstream/13358, chr16-CpG: 61/Downstream/6977

Upstream sequence

tgtttataaaataaatgtgtataatggccgggcatgatggctcaagcctgtaatctcagcactttgggaggccgaggcgggtgtattacgaggccaggag

Downstream sequence

ccgggcgtggtggtgggcgtctgtagtcccagctactcgggaggctgaggcaggagaatggtgtgaacccggtaggcggagtttgcagggagccgagatc

Reference

Liu, Y., et al. Comprehensive mapping of the human papillomavirus (HPV) DNA integration sites in cervical carcinomas by HPV capture technology. Oncotarget,2016, 7(5): 5852-5864.