CDK5RAP2 _LIHC.png
Expression analysis of TCGA samples
Basic Information
VIS ID
TVIS10005160
Fusion event
HBV-CDK5RAP2 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
1820
Orient
+
Integrated sequence
GTTTAAGGACTGGGAGGAGTTGGGGGAGGAGATTAGGTTAAAGGTCTTTGTACTAGGAGGCTGTAGGCATAAATTGGTCTGTTCACCAGCACCATGCAAC| |TTTTTCACCTCTGCCTAATCATCTCATGTTCATGTCCTACTGTTCAAGCCTCCAAGCTGTGCCTTGGGTGGCTTTGGGGCATGGACATTGACCCGTATAA
Host Sequence
Chromosome
chr9
Cytoband
q33.2
Reference genome
GRCh37/hg19
Start
123196448/120434170 (Hg38)
End
123196448/120434170 (Hg38)
Orient
-
Location type
Intron
Target gene
CDK5RAP2
miRNAs that regulate target gene
hsa-mir-1301-3p ; hsa-mir-324-3p ; hsa-mir-149-5p
Nearest miRNA
hsa-let-7a-1/Upstream/189120; hsa-mir-12126/Downstream/1685912;
Nearest TSS
ENST00000422679/Upstream/30508; ENST00000437707/Downstream/6249;
Nearest CpG islands
None/Target, chr9-CpG: 64/Upstream/1064234, chr9-CpG: 40/Downstream/60589
Upstream sequence
AAGCACATAAGCTTTGTAACACTGCTGCTTCTGTTAATCCATTAGATTTAGATCAAAGTTATGGCATCAGATTGAGTCTCAATAATTTAAGAAAAATTAA
Downstream sequence
cataaagagctgtcaaagagcacctcgttaatatgatgacatttgagacaaggcctgaagggatcagggacaccagacagaagagaaagtgcaaagcccc
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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