Basic Information
VIS ID
TVIS20002102
Fusion event
HPV-RARA integration
Validated
No
Detection method
HIVID
Data source
Curated
Sample type
Tumor
Disease
Not given
Quality evaluation
Normal
Reported year
2015
PubMed ID
25581428
Virus Sequence
Virus name
HPV
Reference genome
NC_001526.2;AY262282.1
Host Sequence
Chromosome
chr17
Cytoband
q21.2
Reference genome
GRCh37/hg19
Start
38512144/40355892 (Hg38)
End
38512144/40355892 (Hg38)
Location type
Intronic
Target gene
RARA
miRNAs that regulate target gene
hsa-mir-125a-5p ; hsa-mir-218-5p ; hsa-mir-615-3p ; hsa-mir-138-5p ; hsa-mir-6780a-5p ; hsa-mir-6779-5p ; hsa-mir-3689c ; hsa-mir-3689b-3p ; hsa-mir-3689a-3p ; hsa-mir-30b-3p ; hsa-mir-1273h-5p ; hsa-mir-519e-5p ; hsa-mir-515-5p ; hsa-mir-6778-5p ; hsa-mir-1233-5p ; hsa-mir-6780b-5p ; hsa-mir-4725-3p ; hsa-mir-4271 ; hsa-mir-6799-5p ; hsa-mir-5196-5p ; hsa-mir-7106-5p ; hsa-mir-4747-5p ; hsa-mir-6797-5p ; hsa-mir-1249-5p ; hsa-mir-6133 ; hsa-mir-6130 ; hsa-mir-6129 ; hsa-mir-6127 ; hsa-mir-4510 ; hsa-mir-4419a ; hsa-mir-605-3p ; hsa-mir-3925-3p ; hsa-mir-766-3p ; hsa-mir-194-3p ; hsa-mir-6783-5p ; hsa-mir-4756-5p ; hsa-mir-4739 ; hsa-mir-1321 ; hsa-mir-940 ; hsa-mir-6893-5p ; hsa-mir-3714 ; hsa-mir-6808-5p ; hsa-mir-27a-3p
Nearest miRNA
hsa-mir-1180/Upstream/162229; hsa-mir-10226/Downstream/1161272;
Nearest TSS
ENST00000595228/Upstream/4505; ENST00000578774/Downstream/4763;
Nearest CpG islands
None/Target, chr17-CpG: 26/Upstream/10305, chr17-CpG: 150/Downstream/6821
Nearest cancer related gene
RARA(OG, No orient, 0)
Upstream sequence
TCGAATCCTTTTTCAGCTAATATAATATAGTAAATATTTTTATGATGCTACCTAATTAGagtcatcccttggtatgggaggggaattgtttcccggaccc
Downstream sequence
CAAGAAAGATGCTAATATCAGCAGTATTGATCTTCCCACCTCGAGCCAGGCTTGCTGGGGCTGGGGGTGGGAGGGCTGGCCCAGCGTGCTGACCTCTGCC
Reference
Hu, Z., et al. Genome-wide profiling of HPV integration in cervical cancer identifies clustered genomic hot spots and a potential microhomology-mediated integration mechanism. Nat Genet,2015, 47(2): 158-163.
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