hsa-mir-7-5p _HNSC.png
Expression analysis of TCGA samples
Basic Information
VIS ID
TVIS20004235
Fusion event
HPV-THAP12 integration
Validated
Yes
Detection method
WGS, RNA-seq, Whole-Exome sequencing, PCR
Data source
Curated
Sample type
Tumor
Disease
Head and neck squamous cell carcinoma (HNSCC)
Quality evaluation
Perfect
Reported year
2014
PubMed ID
25313082
Virus Sequence
Virus name
HPV
Subtype
HPV16
Reference genome
AY686584
Gene
E1
Start
2096
Integrated sequence
AATATGCACAATTGGCAGACACTAATAGTAATGCAAGTGCCTTTCTAAAAAGTAATTCACAGGCAAAAATTGTAAAGGATTGTGCAACAATGTGTAGACA| |TTATAAACGAGCAGAAAAAAAACAAATGAGTATGAGTCAATGGATAAAATATAGATGTGATAGGGTAGATGATGGAGGTGATTGGAAGCAAATTGTTATG
Host Sequence
Chromosome
chr11
Cytoband
q13.5
Reference genome
GRCh37/hg19
Start
76083005/76371961 (Hg38)
End
76083005/76371961 (Hg38)
Location type
Intronic
Fragile sites / regions
FRA11H
Target gene
THAP12
miRNAs that regulate target gene
hsa-mir-34a-5p ; hsa-mir-7-5p ; hsa-mir-98-5p ; hsa-mir-24-3p
Nearest miRNA
hsa-mir-10392/Upstream/1036775; hsa-let-7a-2/Downstream/3030061;
Nearest TSS
ENST00000527297/Upstream/3318; ENST00000530460/Downstream/8981;
Nearest CpG islands
None/Target, chr11-CpG: 30/Upstream/49758, chr11-CpG: 103/Downstream/8519
Junction sequence
CATTGACTCATACTCATTTGTTTTTTTTCTGCTCGTTTGTAA---[CCGGG]---CCCCACCATGCCCGGTTAATTTTTGTACTTTTAGTAGAGATGGGGTTTCGCTAT
* Color:  Human Sequence / Virus Sequence / Overlapped sequence / Unknown sequence
Reference
Parfenov, M., et al. Characterization of HPV and host genome interactions in primary head and neck cancers. Proc Natl Acad Sci U S A,2014,111(43): 15544-15549.
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