PFDN1 _LIHC.png
Expression analysis of TCGA samples
Basic Information
VIS ID
TVIS10011746
Fusion event
HBV-PFDN1 integration
Validated
No
Detection method
NGS
Data source
Curated
Sample type
Tumor
Disease
Hepatocellular carcinoma (HCC)
Quality evaluation
Normal
Reported year
2018
PubMed ID
30271481
Virus Sequence
Virus name
HBV
Reference genome
NC_003977
Region type
Polymerase|
Start
2634
Orient
+
Integrated sequence
CACCATCTTTTCCTAATATACATTTACACCAAGACATTATCAAAAAATGTGAACAGTTTGTAGGCCCACTCACAGTTAATGAGAAAAGAAGATTGCAATT| |GATTATGCCTGCCAGGTTTTATCCAAAGGTTACCAAATATTTACCATTGGATAAGGGTATTAAACCTTATTATCCAGAACATCTAGTTAATCATTACTTC
Host Sequence
Chromosome
chr5
Cytoband
q31.3
Reference genome
GRCh37/hg19
Start
139675344/140295759 (Hg38)
End
139675344/140295759 (Hg38)
Orient
-
Location type
Intronic
Target gene
PFDN1
miRNAs that regulate target gene
hsa-mir-122-5p ; hsa-mir-1-3p
Nearest miRNA
hsa-mir-10397/Upstream/2648110; hsa-mir-103a-1/Downstream/267912;
Nearest TSS
ENST00000502646/Upstream/2552; ENST00000514849/Downstream/4824;
Nearest CpG islands
None/Target, chr5-CpG: 87/Upstream/119887, chr5-CpG: 87/Downstream/50186
Upstream sequence
taaaccaggaagaagtcaaatctctgaatagacctatgacaagttctgaaattgagacagtaattaatagcctaccaacaaaaaagcccaggaccagaag
Downstream sequence
TAAGAGGTATTTAACACTACAAAATGTGTCCATACTTATGAAATGAAAGATATCTGGGTCTGCAATGATTTGTTTAACTAAATACATACCCTAAAAAAAA
Reference
Yang, L., et al. Molecular Characterization of HBV DNA Integration in Patients with Hepatitis and Hepatocellular Carcinoma. J Cancer ,2018,9(18): 3225-3235.
Curate