hsa-mir-21-5p _CESC.png
PDGFD _CESC.png
Expression analysis of TCGA samples
Basic Information
VIS ID
TVIS20000056
Fusion event
HPV-PDGFD integration
Validated
Yes
Detection method
PCR and Sanger sequencing
Data source
Curated
Sample type
Tumor
Disease
Cervical carcinoma (CC)
Quality evaluation
Normal
Reported year
2016
PubMed ID
26735580
Virus Sequence
Virus name
HPV
Subtype
HPV16
Reference genome
NC_001526.4
Gene
L1
Start
5745
Integrated sequence
ATTTTCCTACACCTAGTGGTTCTATGGTTACCTCTGATGCCCAAATATTCAATAAACCTTATTGGTTACAACGAGCACAGGGCCACAATAATGGCATTTG| |TTGGGGTAACCAACTATTTGTTACTGTTGTTGATACTACACGCAGTACAAATATGTCATTATGTGCTGCCATATCTACTTCAGAAACTACATATAAAAAT
Host Sequence
Chromosome
chr11
Cytoband
q22.3
Reference genome
GRCh37/hg19
Start
103893590/104022862 (Hg38)
End
103893590/104022862 (Hg38)
Location type
Intronic
Target gene
PDGFD
miRNAs that regulate target gene
hsa-mir-21-5p ; hsa-mir-145-5p
Nearest miRNA
hsa-mir-10392/Upstream/172882; hsa-let-7a-2/Downstream/7324895;
Nearest TSS
ENST00000527297/Upstream/77314; ENST00000302259/Downstream/13718;
Nearest CpG islands
None/Target, chr11-CpG: 30/Upstream/930542, chr11-CpG: 43/Downstream/13815
Upstream sequence
ATAAACTTTTGTTTTCttattttttattagtaattattatatgtatttatgggatacaatgtggtgttttgataaatgtatacatcatgaaattattaaa
Downstream sequence
caagcaattagtttaataaatacagatctattcctattttccattttctatttctattatcttgtatcaattttagtaggttgtgcttttcaggatgtga
Reference
Liu, Y., et al. Comprehensive mapping of the human papillomavirus (HPV) DNA integration sites in cervical carcinomas by HPV capture technology. Oncotarget,2016, 7(5): 5852-5864.
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