Basic Information
VIS ID
TVIS20004408
Fusion event
HPV-SGSM1 integration
Validated
Yes
Detection method
DIPS-PCR
Data source
Curated
Sample type
Tumor
Disease
Oropharyngeal squamous cell carcinoma (OSCC)
Quality evaluation
Normal
Reported year
2014
PubMed ID
24586376
Virus Sequence
Virus name
HPV
Subtype
HPV16
Reference genome
NC_001526.1
Gene
E1
Start
1334
Integrated sequence
GAGATTATTTGAAAGCGAAGACAGCGGGTATGGCAATACTGAAGTGGAAACTCAGCAGATGTTACAGGTAGAAGGGCGCCATGAGACTGAAACACCATGT| |AGTCAGTATAGTGGTGGAAGTGGGGGTGGTTGCAGTCAGTACAGTAGTGGAAGTGGGGGAGAGGGTGTTAGTGAAAGACACACTATATGCCAAACACCAC
Host Sequence
Chromosome
chr22
Cytoband
q11.23
Reference genome
GRCh37.p5
Start
25233023/24837056 (Hg38)
End
25233023/24837056 (Hg38)
Orient
-
Location type
Intron1
Target gene
SGSM1
miRNAs that regulate target gene
hsa-mir-760 ; hsa-mir-221-5p ; hsa-mir-6848-3p ; hsa-mir-3187-3p ; hsa-mir-6843-3p ; hsa-mir-4435 ; hsa-mir-588 ; hsa-mir-4701-5p ; hsa-mir-548s ; hsa-mir-6131 ; hsa-mir-4755-3p ; hsa-mir-3663-5p ; hsa-mir-372-5p ; hsa-mir-371a-5p ; hsa-mir-616-5p ; hsa-mir-373-5p ; hsa-mir-371b-5p ; hsa-mir-548o-3p ; hsa-mir-1323 ; hsa-mir-4781-3p
Nearest miRNA
hsa-mir-1286/Upstream/1950677; hsa-let-7a-3/Downstream/618590;
Nearest TSS
ENST00000624155/Upstream/30737; ENST00000480523/Downstream/6404;
Nearest CpG islands
None/Target, chr22-CpG: 279/Upstream/30470, chr22-CpG: 147/Downstream/115128
Upstream sequence
CTATTTCACGGGTTGCCGTTTTCACTGTTTATTTTGTTCTTTGATCCACAAAAAGTTTTAACTTTGCTGTCCAGTTTACCTATTTTTAATTTTGTTGCTC
Downstream sequence
AGAGTGTAGAAATAAAGACACAAGACAAAGAGACAAGAGAAAAGGCAGCTGGGCCCGGGGGACCACTACCACCAATGCACGGAGACCGGTAGTGGCCCCA
Target sequence
ATGCATTTGGTGTCATATCCAAGAAATCATTGTCAAATCCAATGTTGTAGGGACCAGCCCCACAGGGTCGGTGGGTCTCTCCCTGTGTGCGGCAACAAG
Reference
Olthof, N. C., et al.Comprehensive analysis of HPV16 integration in OSCC reveals no significant impact of physical status on viral oncogene and virally disrupted human gene expression.2014, PLoS One 9(2): e88718.
Curate