Basic Information
VIS ID
TVIS20003803
Fusion event
HPV-ROCK1 integration
Validated
Yes
Detection method
PCR and Sanger sequencing
Data source
Curated
Sample type
Cell line
Disease
Not given
Quality evaluation
Perfect
Reported year
2015
PubMed ID
25581428
Virus Sequence
Virus name
HPV
Subtype
HPV16
Reference genome
NC_001526.2
Start
4471
End
4444
Orient
+
Integrated sequence
TGGGTATATTCCATTGGGAACAAGGCCT
Host Sequence
Chromosome
chr18
Cytoband
q11.1
Reference genome
GRCh37/hg19
Start
18518922/20938961 (Hg38)
End
18518922/20938961 (Hg38)
Location type
Intronic
Target gene
ROCK1
miRNAs that regulate target gene
hsa-mir-146a-5p ; hsa-mir-584-5p ; hsa-mir-124-3p ; hsa-mir-1280 ; hsa-mir-148b-3p ; hsa-mir-335-5p ; hsa-mir-148a-3p ; hsa-mir-135a-5p ; hsa-mir-145-5p ; hsa-mir-340-5p ; hsa-mir-4662a-5p ; hsa-mir-4753-5p ; hsa-mir-6507-5p ; hsa-mir-6768-3p ; hsa-mir-548aw ; hsa-mir-5093 ; hsa-mir-1468-3p ; hsa-mir-548x-5p ; hsa-mir-548g-5p ; hsa-mir-548f-5p ; hsa-mir-548aj-5p ; hsa-mir-3688-3p ; hsa-mir-300 ; hsa-mir-506-3p ; hsa-mir-584-3p ; hsa-mir-126-3p ; hsa-mir-144-5p
Nearest miRNA
hsa-mir-3156-2/Upstream/6108719; hsa-mir-1-2/Downstream/744557;
Nearest TSS
ENST00000575820/Upstream/5774494; ENST00000579454/Downstream/15909;
Nearest CpG islands
None/Target, chr18-CpG: 67/Upstream/5607786, chr18-CpG: 113/Downstream/172018
Nearest cancer related gene
ROCK1(OG, No orient, 0)
Downstream sequence
ACATTTCGAGCGCTTTGAGACCTACGGTGGAAAAGGAATTATCTTCCCATAAAAAATAGACAGAAGCATTCTCAGAATCATGTTTGTGATGTGTGTACTCA
Junction sequence
GCCTTGTTCCCAATGGAATATACCCAGTACATTTCGAGCGCTTTGAGACCTACGGTGGAAAAGGAATTATCTTCCCATAAAAAATAGACAGAAGCATTCTCAGAATCATGTTTGTGATGTGTGTACTCA
* Color:  Human Sequence / Virus Sequence / Overlapped sequence / Unknown sequence
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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