hsa-mir-215-5p _CESC.png
RFC4 _CESC.png
Expression analysis of TCGA samples
Basic Information
VIS ID
TVIS20004188
Fusion event
HPV-RFC4 integration
Validated
Yes
Detection method
APOT and sequencing
Data source
Curated
Sample type
Cell line
Disease
Cervical carcinoma (CC)
Quality evaluation
Good
Reported year
2018
PubMed ID
29364907
Virus Sequence
Virus name
HPV
Subtype
HPV16
Reference genome
AF125673.1
Strand
+
Gene
E1/E2
Start
2788
End
3018
Orient
+
Integrated sequence
CAGGACAAAATACTAACACATTATGAAAATGATAGTACAGACCTACGTGACCATATAGACTATTGGAAACACATGCGCCTAGAATGTGCTATTTATTACAAGGCCAGAGAAATGGGATTTAAACATATTAACCACCAGGTGGTGCCAACACTGGCTGTATCAAAGAATAAAGCATTACAAGCAATTGAACTGCAACTAACGTTAGAAACAATATATAACTCACAATATAGT
Host Sequence
Chromosome
chr3
Cytoband
q27.3
Reference genome
GRCh37/hg19
Start
186507881/186790092 (Hg38)
End
186508213/186790424 (Hg38)
Orient
-
Location type
Intronic
Fragile sites / regions
FRA3C
Target gene
RFC4
miRNAs that regulate target gene
hsa-mir-193b-3p ; hsa-mir-215-5p ; hsa-mir-192-5p
Nearest miRNA
hsa-let-7g/Upstream/3315; hsa-mir-28/Downstream/1898357;
Nearest TSS
ENST00000440867/Upstream/2316; ENST00000434957/Downstream/1426;
Nearest CpG islands
None/Target, chr3-CpG: 148/Upstream/5833, chr3-CpG: 60/Downstream/15882
Nearby gene
EIF4A2(-196) ;
Downstream sequence
GGTATTAAAGATGTTTCTAGGTGAGACTAGACATACACTCTGCCAACTGGCCCCCGTGCCCCCAGTCATTTCTGTTCCACACCTAAGTTCCATACTTTCC
Target sequence
CCTTCAGGTAGTTAAATGTTCCATTGACATGTGCAAAGTACCTACTTACGGCAAGTTTTTCTGTGATAATAGACTTCTGTTTATCAGATAAGTTATTTTCTACAACCACATCATGGAGTTGATTGACGAGCTGAGTTGCTGCATGACCCTCATCTATTAAATCCTATAATAAAAAAAACTTTTGGTATGATGACTTAATATTCCTTTCCCCAAAGTTAGTAAGCTGACTTTACCTTGACCACAGCTTCTAGTTTG
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.
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