Expression analysis of TCGA samples
Basic Information
VIS ID
TVIS20004165
Fusion event
HPV-CDC42 integration
Validated
Yes
Detection method
APOT and sequencing
Data source
Curated
Sample type
Disease
Cervical carcinoma (CC)
Quality evaluation
Good
Reported year
2018
PubMed ID
Virus Sequence
Virus name
HPV
Subtype
HPV16
Reference genome
Strand
-
Gene
L2
Start
4177
End
4385
Orient
-
Integrated sequence
TATATATTTTTTTTTTGTTTGTTTGTTTGTTTTTTAATAAACTGTTATCACTTAACAATGCGACACAAACGTTCTGCAAAACGCACAAAACGTGCATCGGCTACCCAACTTTATAAAACATGCAAACAGGCAGGTACATGTCCACCTGACATTATACCTAAGGTTGAAGGCAAAACTATTGCTGATCAAATATTACAATATGGAAGTAT
Host Sequence
Chromosome
chr1
Cytoband
p36.12
Reference genome
Start
End
22381464/22054971 (Hg38)
Orient
+
Location type
Intronic
Fragile sites / regions
Target gene
miRNAs that regulate target gene
hsa-mir-133a-3p ; hsa-mir-224-5p ; hsa-mir-185-5p ; hsa-mir-137 ; hsa-mir-216a-5p ; hsa-mir-330-3p ; hsa-mir-608 ; hsa-mir-29b-3p ; hsa-mir-29c-3p ; hsa-mir-29a-3p ; hsa-mir-195-5p ; hsa-mir-375 ; hsa-mir-1-3p ; hsa-mir-93-3p ; hsa-mir-484 ; hsa-mir-106b-5p ; hsa-mir-133b ; hsa-mir-204-5p ; hsa-mir-20a-3p ; hsa-mir-1207-3p ; hsa-mir-3914 ; hsa-mir-3591-3p ; hsa-mir-21-3p ; hsa-mir-107 ; hsa-mir-30c-5p
Nearest miRNA
hsa-mir-12136/Upstream/1066481; hsa-mir-101-1/Downstream/211268;
Nearest CpG islands
None/Target, chr1-CpG: 111/Upstream/1377, chr1-CpG: 35/Downstream/65056
Upstream sequence
ttcaagaaactatgccgtaaaacagatgtgctgtcatctagtcttttttgtttcacttatagaacacagtagatttagcataattctcaagggccctggg
Downstream sequence
gagaaggagtctcgctctgtctcccaggctggagtgcagtggcgcaatctcagctcactgcaagctccgcctcccaggttcacaccattctcctgcctca
Target sequence
tatatatatttttttttttttttttttttttttttttttttttttttttttttttttt
Reference
Warburton, A., et al. HPV integration hijacks and multimerizes a cellular enhancer to generate a viral-cellular super-enhancer that drives high viral oncogene expression. PLoS Genet ,2018,14(1): e1007179.