Expression analysis of TCGA samples
Basic Information
VIS ID
TVIS20004506
Fusion event
HPV-CSMD3 integration
Validated
Yes
Detection method
Multiplex RT-PCR, APOT assay
Data source
Curated
Sample type
Disease
Cervical carcinoma (CC)
Quality evaluation
Normal
Reported year
2014
PubMed ID
Virus Sequence
Virus name
HPV
Subtype
HPV16
Reference genome
Gene
E1
Start
2686
Integrated sequence
TAATTACATCTAACATTAATGCTGGTACAGATTCTAGGTG GCCTTATTTACATAATAGATTGGTGGTGTTTACATTTCCTAATGAGTTTCCATTTGACG| |AAAACGGAAAT CCAGTGTATGAGCTTAATGATAAGAACTGGAAATCCTTTTTCTCAAGGACGTGGTCCAGATTAAGTTTGC ACGAGGACGAGGACAAG
Host Sequence
Chromosome
chr8
Cytoband
q23.3
Reference genome
End
113482518/112470289 (Hg38)
Location type
Intronic
Target gene
Nearest miRNA
hsa-mir-12123/Upstream/7985824; hsa-mir-10400/Downstream/173204;
Nearest CpG islands
None/Target, chr8-CpG: 109/Upstream/2494446, chr8-CpG: 21/Downstream/962308
Upstream sequence
AGCAATTTCATAATCTCAGATCATCTCAGAGTTCGTGTGGCTTTCAGCTCTCTCTCTCTCTCTCTGGCATTTAAAAAATCAATGTAATTTCAAACACAAA
Downstream sequence
ATTTAACCTTTTTCGGGGGTGGAAGAGGGGATAGGGGAAGTTTTATATGAATGTGAACATAAAGAAGAATGTGTATATGTGTACTTGTGTATGCATGTGA
Reference
Lu, X., et al. Multiple-integrations of HPV16 genome and altered transcription of viral oncogenes and cellular genes are associated with the development of cervical cancer. PLoS One ,2014,9(7): e97588.