PCDH11Y _LIHC.png
Expression analysis of TCGA samples
Basic Information
VIS ID
TVIS10005083
Fusion event
HBV-PCDH11Y integration
Validated
No
Detection method
PCR and Ultra-deep sequencing
Data source
Curated
Sample type
Nontumor
Disease
Hepatocellular carcinoma (HCC)
Quality evaluation
Normal
Reported year
2018
PubMed ID
29861854
Virus Sequence
Virus name
HBV
Reference genome
AP011098
Start
1564
Orient
+
Integrated sequence
CGGGGCCGTTTGGGGCTCTACCGTCCCCTTCTTCATCTGCCGTTCCGGCCGACCACGGGGCGCACCTCTCTTTACGCGGTCTCCCCGTCTGTGCCTTCTC| |ATCTGCCGGACCGTGTGCACTTCGCTTCACCTCTGCACGTCGCATGGAGACCACCGTGAACGCCCACCAGGTCTTGCCCAAGGTCTTACATAAGAGGACT
Host Sequence
Chromosome
chrY
Cytoband
p11.2
Reference genome
GRCh37/hg19
Start
5482026/5613985 (Hg38)
End
5482026/5613985 (Hg38)
Orient
-
Location type
Intron
Target gene
PCDH11Y
miRNAs that regulate target gene
hsa-mir-574-5p ; hsa-mir-297 ; hsa-mir-6867-5p ; hsa-mir-223-5p ; hsa-mir-567 ; hsa-mir-376a-2-5p ; hsa-mir-3935 ; hsa-mir-511-3p ; 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-mir-3690-2/Upstream/1007757; hsa-mir-12120/Downstream/7865192;
Nearest TSS
ENST00000430575/Upstream/557895; ENST00000429039/Downstream/632238;
Nearest CpG islands
None/Target, chrY-CpG: 62/Upstream/610801, chrY-CpG: 41/Downstream/632038
Upstream sequence
taaggtctggagacatacagagttagccagattccctggctaggctgggaagagtcagacattgtatgcagctttgtctttgtcatgggctctgcaatgt
Downstream sequence
TGAATAGTTCACCAGTATTTGTCAGCACAACAGAACATAAACATTTGTATTGCTGGGTGCTCATTTTACAGTTGTTTATAGAGACTACAGGGTGCCATTC
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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