Expression analysis of TCGA samples
Basic Information
VIS ID
TVIS20004535
Fusion event
HPV-ARID3A 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
E2
Start
2019
Integrated sequence
ACAGTATTACAACATAGTTTTAATGATTGTACATTTGAATTATCACAGATGGTACAATGGGCCTACGA TAATGACATAGTAGACGATAGTGAAATTGCA| |TATAAATATGCACAATTGGCAGACACTAATAGTAATGCA AGTGCCTTTCTAAAAAGTAATTCACAGGCAAAAATTGTAAAGGATTGTGCAACAATGTGT
Host Sequence
Chromosome
chr19
Cytoband
p13.3
Reference genome
Start
End
963052/963052 (Hg38)
Location type
Intronic
Fragile sites / regions
Target gene
miRNAs that regulate target gene
hsa-let-7b-5p ; hsa-mir-30b-5p ; hsa-mir-98-5p ; hsa-let-7d-5p ; hsa-mir-484 ; hsa-mir-425-3p ; hsa-mir-125b-5p ; hsa-mir-30a-5p ; hsa-mir-148a-3p ; hsa-mir-30c-5p ; hsa-mir-30d-5p ; hsa-mir-152-3p ; hsa-mir-30e-5p ; hsa-mir-148b-3p ; hsa-mir-3171 ; hsa-mir-6757-5p ; hsa-mir-8485 ; hsa-let-7c-5p ; hsa-mir-6722-3p ; hsa-mir-1909-3p ; hsa-mir-6836-5p ; hsa-mir-6132 ; hsa-mir-202-3p ; hsa-mir-4500 ; hsa-let-7f-5p ; hsa-let-7g-5p ; hsa-mir-4458 ; hsa-let-7i-5p ; hsa-let-7a-5p ; hsa-let-7e-5p ; hsa-mir-1277-5p ; hsa-mir-190a-3p ; hsa-mir-5011-5p ; hsa-mir-6083 ; hsa-mir-4753-3p ; hsa-mir-130b-5p ; hsa-mir-1238-3p ; hsa-mir-670-3p ; hsa-mir-6749-3p ; hsa-mir-6792-3p ; hsa-mir-4691-5p ; hsa-mir-660-3p ; hsa-mir-5193 ; hsa-mir-7856-5p ; hsa-mir-556-3p ; hsa-mir-6809-3p ; hsa-mir-99b-5p ; hsa-mir-125a-5p ; hsa-mir-129-5p ; hsa-mir-3140-3p ; hsa-mir-6885-3p
Nearest miRNA
hsa-mir-1302-11/Upstream/149399; hsa-let-7e/Downstream/853107;
Nearest CpG islands
None/Target, chr19-CpG: 112/Upstream/12682, chr19-CpG: 43/Downstream/19637
Nearest cancer related gene
ARID3A(OG, No orient, 0)
Upstream sequence
ggcaggagaatagtgtgaatccaggaggtggagcttgcagtgagctgagattgtgccactgcactccagcctgcacaacaaagcgagactccgtttcagg
Downstream sequence
GCGGAGGGTGGTGGGAGGTGTTTCTGGAAGGTCAGACACCGGGGGTTCCGGGGGTAGCAGGCCTCGACCAGGCAGAGGGCCGGCTGCTCACTCAGGGCTG
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.