PALMD _LIHC.png
Expression analysis of TCGA samples
Basic Information
VIS ID
TVIS10008493
Fusion event
HBV-PALMD integration
Validated
No
Detection method
NGS
Data source
Curated
Sample type
Nontumor
Disease
Hepatocellular carcinoma (HCC)
Quality evaluation
Normal
Reported year
2018
PubMed ID
30271481
Virus Sequence
Virus name
HBV
Reference genome
NC_003977
Region type
precore/core protein|
Start
1855
Orient
+
Integrated sequence
TAGGTTAAAGGTCTTTGTACTAGGAGGCTGTAGGCATAAATTGGTCTGCGCACCAGCACCATGCAACTTTTTCACCTCTGCCTAATCATCTCTTGTTCAT| |GTCCTACTGTTCAAGCCTCCAAGCTGTGCCTTGGGTGGCTTTGGGGCATGGACATCGACCCTTATAAAGAATTTGGAGCTACTGTGGAGTTACTCTCGTT
Host Sequence
Chromosome
chr1
Cytoband
p21.2
Reference genome
GRCh37/hg19
Start
100148774/99683218 (Hg38)
End
100148774/99683218 (Hg38)
Orient
-
Location type
Intronic
Fragile sites / regions
FRA1M
Target gene
PALMD
miRNAs that regulate target gene
hsa-mir-98-5p
Nearest miRNA
hsa-mir-101-1/Upstream/1637047; hsa-mir-11399/Downstream/598023;
Nearest TSS
ENST00000473358/Upstream/15638; ENST00000496843/Downstream/48;
Nearest CpG islands
None/Target, chr1-CpG: 111/Upstream/418439, chr1-CpG: 63/Downstream/166646
Upstream sequence
aaagaaagaaagaaagaaagaaagaaagaaagaaagaaagaaagaaagaaaCGAACACCCTATGAAGTTGTTAACATTGAccagatctctaaatgttgaa
Downstream sequence
ttgctccagattcaggccttggaattcttatctccttcactttctagggaaacttatccactcctgtggtgataaataccaactcccaaatgtatatctt
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.
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