CDKN2C _LIHC.png
Expression analysis of TCGA samples
Basic Information
VIS ID
TVIS10004818
Fusion event
HBV-CDKN2C 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
1805
Orient
+
Integrated sequence
CTTCAAAGACTGTTTGTTTAAGGACTGGGAGGAGTTGGGGGAGGAGATTAGGTTAAAGGTCTTTGTACTAGGAGGCTGTAGGCATAAATTGGTCTGTTCA| |CCAGCACCATGCAACTTTTTCACCTCTGCCTAATCATCTCATGTTCATGTCCTACTGTTCAAGCCTCCAAGCTGTGCCTTGGGTGGCTTTGGGGCATGGA
Host Sequence
Chromosome
chr1
Cytoband
p32.3
Reference genome
GRCh37/hg19
Start
51436795/50971123 (Hg38)
End
51436795/50971123 (Hg38)
Orient
-
Location type
Intron
Fragile sites / regions
FRA1B
Target gene
CDKN2C
miRNAs that regulate target gene
hsa-mir-34a-5p ; hsa-mir-218-5p ; hsa-mir-4740-3p
Nearest miRNA
hsa-mir-12136/Upstream/6425571; hsa-mir-101-1/Downstream/88714;
Nearest TSS
ENST00000473358/Upstream/1179; ENST00000474016/Downstream/131111;
Nearest CpG islands
None/Target, chr1-CpG: 111/Upstream/1290, chr1-CpG: 79/Downstream/6516
Nearest cancer related gene
CDKN2C(TSG, No orient, 0)
Upstream sequence
ACATTTTACAGTTAATGTAATACCATCCACTCATTCAGGAGTCGGGAGGAATAAAAAGTTGAATTTTCTAATCAGAGCTCAGCTGCAGTGTCTTTGTCTC
Downstream sequence
TACGGTCATGCCGTGGTGTGCTCTAATTTTCAGTAATTAGATTTACAGGCAACAATTGACACATGTCCAGCTGCCAAGTATTGTACCTGATAATTTTTTT
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).
Curate