Basic Information
VIS ID
TVIS20003709
Fusion event
HPV-SEMA3D integration
Validated
Yes
Detection method
PCR and Sanger sequencing
Data source
Curated
Sample type
Tumor
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
1092
End
1171
Orient
+
Integrated sequence
AAACAACATAGAGATGCAGTACAGGTTCTAAAACGAAAGTATTTGGTAGTCCACTTAGTGATATTAGTGGATGTGTAGAC
Host Sequence
Chromosome
chr7
Cytoband
q21.11
Reference genome
GRCh37/hg19
Start
84949539/85320223 (Hg38)
End
84949539/85320223 (Hg38)
Location type
Intronic
Target gene
SEMA3D
miRNAs that regulate target gene
hsa-mir-193a-3p ; hsa-mir-628-5p ; hsa-mir-203a-3p ; hsa-mir-892c-5p ; hsa-mir-302f ; hsa-mir-3646 ; hsa-mir-2053 ; hsa-mir-1468-5p ; hsa-mir-590-3p
Nearest miRNA
hsa-mir-10525/Upstream/9404954; hsa-mir-10399/Downstream/6883792;
Nearest TSS
ENST00000635602/Upstream/133368; ENST00000422448/Downstream/100899;
Nearest CpG islands
None/Target, chr7-CpG: 39/Upstream/133297, chr7-CpG: 45/Downstream/1466081
Downstream sequence
AAAATAATAGCAACTATTCCTACCCATAGCACTCAACTGTATATAGATTACCTCATTCAAACCTCAAAACATCCTTATTGGTCTAGAAAA
Junction sequence
AAAACAACATAGAGATGCAGTACAGGTTCTAAAACGAAAGTATTTGGGTAGTCCACTTAGTGATATTAGTGGATGTGTAGAAAATAATAGCAACTATTCCTACCCATAGCACTCAACTGTATATAGATTACCTCATTCAAACCTCAAAACATCCTTATTGGTCTAGAAAA
* 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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