Basic Information
VIS ID
TVIS20003790
Fusion event
HPV-CDK13 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
3205
End
3222
Orient
-
Integrated sequence
AAGTTGACTATTATGGTT
Host Sequence
Chromosome
chr7
Cytoband
p14.1
Reference genome
GRCh37/hg19
Start
40041141/40001542 (Hg38)
End
40041141/40001542 (Hg38)
Location type
Intronic
Target gene
CDK13
miRNAs that regulate target gene
hsa-mir-133b ; hsa-mir-29b-2-5p ; hsa-mir-4659b-3p ; hsa-mir-4659a-3p ; hsa-mir-6875-3p ; hsa-mir-664b-3p ; hsa-mir-579-3p ; hsa-mir-5696 ; hsa-mir-664a-3p ; hsa-mir-30e-3p ; hsa-mir-30d-3p ; hsa-mir-30a-3p ; hsa-mir-8061 ; hsa-mir-4760-5p ; hsa-mir-6794-3p ; hsa-mir-376a-5p ; hsa-mir-372-5p ; hsa-mir-888-5p
Nearest miRNA
hsa-mir-1183/Upstream/3082110; hsa-mir-10399/Downstream/3149353;
Nearest TSS
ENST00000635602/Upstream/2153; ENST00000642592/Downstream/44388;
Nearest CpG islands
None/Target, chr7-CpG: 39/Upstream/49529, chr7-CpG: 109/Downstream/132740
Upstream sequence
TGCTGTATTGGAAGCCTTCCTTTTCTTATCCAGACGTACTTTTTTAAGGCTACCATTTCTCCTATTAAGGAATTTAATAAAATCAGGTTACCAGTTAACAAAAGCAGATGACATTTTTCTTAACTTTAAATGTATTTTAATTCAATTCTGTTCTTATTTCTCAAAAATAGAACCACAAAGTATGTTTCAGTTTCCAATATACCAAATAATATTTATAGTTCAAAAAATTAAGTCTGTCATTAAACAAATTATGGA
Junction sequence
TGCTGTATTGGAAGCCTTCCTTTTCTTATCCAGACGTACTTTTTTAAGGCTACCATTTCTCCTATTAAGGAATTTAATAAAATCAGGTTACCAGTTAACAAAAGCAGATGACATTTTTCTTAACTTTAAATGTATTTTAATTCAATTCTGTTCTTATTTCTCAAAAATAGAACCACAAAGTATGTTTCAGTTTCCAATATACCAAATAATATTTATAGTTCAAAAAATTAAGTCTGTCATTAAACAAATTATGGA
* 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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