Basic Information
VIS ID
TVIS20003688
Fusion event
HPV-KLF12 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
HPV18
Reference genome
AY262282.1
Start
3347
End
3411
Orient
+
Integrated sequence
AGTGAATGTGAAAAATATGGGAACACAGGTACGTGGGAAGTACATTTTGGGAATAATGTAATTGA
Host Sequence
Chromosome
chr13
Cytoband
q22.1
Reference genome
GRCh37/hg19
Start
74232611/73658474 (Hg38)
End
74232611/73658474 (Hg38)
Location type
Intronic
Fragile sites / regions
FRA13E
Target gene
KLF12
miRNAs that regulate target gene
hsa-mir-101-3p ; hsa-mir-23a-3p ; hsa-mir-4652-3p ; hsa-mir-4743-3p ; hsa-mir-218-5p ; hsa-mir-4679 ; hsa-mir-4677-3p ; hsa-mir-216b-5p ; hsa-mir-1264 ; hsa-mir-6888-3p ; hsa-mir-4775 ; hsa-mir-215-3p ; hsa-mir-6773-3p ; hsa-mir-34a-5p ; hsa-mir-141-3p ; hsa-mir-137 ; hsa-mir-200a-3p ; hsa-mir-4720-3p ; hsa-mir-4804-3p
Nearest miRNA
hsa-mir-1297/Upstream/7440150; hsa-mir-1267/Downstream/4039538;
Nearest TSS
ENST00000623511/Upstream/10221; ENST00000419499/Downstream/336575;
Nearest CpG islands
None/Target, chr13-CpG: 551/Upstream/598242, chr13-CpG: 31/Downstream/475498
Downstream sequence
TCAGTAATGCTTTTGTAGCCAGCTGGCAGCCTGCATCCTCACTCACAATTTGGTTCCCTGTTGGTTATTGGCAGGGGCTAGCAAC
Junction sequence
AAGTGAATGTGAAAAATATGGGAACACAGGTACGTGGGAAGTACATTTTGGGAATAATGTAATTGATTCAGTAATGCTTTTGTAGCCAGCTGGCAGCCTGCATCCTCACTCACAATTTGGTTCCCTGTTGGTTATTGGCAGGGGCTAGCAAC
* 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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