PCDH11X _LIHC.png
Expression analysis of TCGA samples
Basic Information
VIS ID
TVIS10004811
Fusion event
HBV-PCDH11X integration
Validated
No
Detection method
PCR and Ultra-deep sequencing
Data source
Curated
Sample type
Tumor
Disease
Hepatocellular carcinoma (HCC)
Quality evaluation
Normal
Reported year
2018
PubMed ID
29861854
Virus Sequence
Virus name
HBV
Reference genome
AP011098
Start
1829
Orient
-
Integrated sequence
CTGGGAGGAGTTGGGGGAGGAGATTAGGTTAAAGGTCTTTGTACTAGGAGGCTGTAGGCATAAATTGGTCTGTTCACCAGCACCATGCAACTTTTTCACC| |TCTGCCTAATCATCTCATGTTCATGTCCTACTGTTCAAGCCTCCAAGCTGTGCCTTGGGTGGCTTTGGGGCATGGACATTGACCCGTATAAAGAATTTGG
Host Sequence
Chromosome
chrX
Cytoband
q21.31
Reference genome
GRCh37/hg19
Start
91770215/92515216 (Hg38)
End
91770215/92515216 (Hg38)
Orient
+
Location type
Intron
Target gene
PCDH11X
miRNAs that regulate target gene
hsa-mir-6867-5p ; hsa-mir-574-5p ; hsa-mir-376a-2-5p ; hsa-mir-3935 ; hsa-mir-2115-3p ; hsa-mir-5694 ; hsa-mir-383-5p ; hsa-mir-432-3p ; hsa-mir-4775 ; hsa-mir-324-5p ; hsa-mir-1306-5p ; hsa-mir-590-3p
Nearest miRNA
hsa-let-7f-2/Upstream/6611509; hsa-mir-105-1/Downstream/2547925;
Nearest TSS
ENST00000429181/Upstream/679711; ENST00000332647/Downstream/1158352;
Nearest CpG islands
None/Target, chrX-CpG: 62/Upstream/732946, chrX-CpG: 20/Downstream/1158331
Upstream sequence
ttgtacatagttttggatacatgtatatatttggatacatatacacaatgtgtaatgatcaagtcagggtaatcaggatacccatcacttcaaatatttg
Downstream sequence
GTCAATTCTCATTTCTTATTATTTCATAAAGAATATTTTTGCAAATACCCTAAGTTAATAAGTCTAGAATTCAAAGTCCAAATGTCCAAATGTTCTTATG
Reference
Tu, T., et al. Hepatitis B Virus DNA Integration Occurs Early in the Viral Life Cycle in an In Vitro Infection Model via Sodium Taurocholate Cotransporting Polypeptide-Dependent Uptake of Enveloped Virus Particles. J Virol ,2018,92(11).
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