Basic Information
VIS ID
TVIS20003793
Fusion event
HPV-MDN1 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
5617
End
5669
Orient
-
Integrated sequence
TTTACCATATTTTTTTTCAGATGTCTCTTTGGCTGCCTAGTGAGGCCACTGTC
Host Sequence
Chromosome
chr6
Cytoband
q15
Reference genome
GRCh37/hg19
Start
90350635/89640916 (Hg38)
End
90350635/89640916 (Hg38)
Location type
Intronic
Fragile sites / regions
FRA6G
Target gene
MDN1
miRNAs that regulate target gene
hsa-mir-16-5p ; hsa-mir-642a-5p ; hsa-mir-484 ; hsa-mir-186-5p ; hsa-mir-222-3p ; hsa-mir-92a-3p ; hsa-mir-1260b ; hsa-mir-6875-3p ; hsa-mir-3685 ; hsa-mir-155-3p ; hsa-mir-7848-3p ; hsa-mir-8485 ; hsa-mir-7153-5p ; hsa-mir-146b-5p ; hsa-mir-146a-5p ; hsa-mir-589-5p ; hsa-mir-362-3p ; hsa-mir-329-3p
Nearest miRNA
hsa-mir-10398/Upstream/11101607; hsa-mir-1202/Downstream/671826;
Nearest TSS
ENST00000381078/Upstream/2163; ENST00000438877/Downstream/3277;
Nearest CpG islands
None/Target, chr6-CpG: 120/Upstream/2071, chr6-CpG: 52/Downstream/178502
Upstream sequence
TGCAGCATTCTTTGTTAGCACTATATTGAACTTAGAGGTTTTCCTGCCCAAAGCATGAGTCTTTGAGCAAGGAGCATATGTGACTCACGACAGCATTACCAG
Junction sequence
TGCAGCATTCTTTGTTAGCACTATATTGAACTTAGAGGTTTTCCTGCCCAAAGCATGAGTCTTTGAGCAAGGAGCATATGTGACTCACGACAGCATTACCAGACAGTGGCCTCACTAGGCAGCCAAAGAGACATCTGAAAAAAAATATGGTAAACGTTTACGTCGTTTTCGTAACATGTAATAACTAGGATGTAAATAAAAGTCCCTGCA
* 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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