CSMD2 _LIHC.png
Expression analysis of TCGA samples
Basic Information
VIS ID
TVIS10006269
Fusion event
HBV-CSMD2 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
1822
Orient
+
Integrated sequence
TTAAGGACTGGGAGGAGTTGGGGGAGGAGATTAGGTTAAAGGTCTTTGTACTAGGAGGCTGTAGGCATAAATTGGTCTGTTCACCAGCACCATGCAACTT| |TTTCACCTCTGCCTAATCATCTCATGTTCATGTCCTACTGTTCAAGCCTCCAAGCTGTGCCTTGGGTGGCTTTGGGGCATGGACATTGACCCGTATAAAG
Host Sequence
Chromosome
chr1
Cytoband
p35.1
Reference genome
GRCh37/hg19
Start
34610888/34145287 (Hg38)
End
34610888/34145287 (Hg38)
Orient
-
Location type
Intron
Target gene
CSMD2
miRNAs that regulate target gene
hsa-mir-3941 ; hsa-mir-125b-2-3p ; hsa-mir-603 ; hsa-mir-362-3p ; hsa-mir-329-3p ; hsa-mir-8485 ; hsa-mir-495-5p ; hsa-mir-4650-5p ; hsa-mir-1972
Nearest miRNA
hsa-mir-12136/Upstream/812795; hsa-mir-101-1/Downstream/524312;
Nearest TSS
ENST00000473358/Upstream/269821; ENST00000373374/Downstream/19987;
Nearest CpG islands
None/Target, chr1-CpG: 111/Upstream/511768, chr1-CpG: 160/Downstream/17895
Upstream sequence
TGAGGTCCTAAGAAGATGCCTTTTCCCAGGGCCAAAGAACAGAACCACCCAAGTTAGGAAAGTGTATAGCTCATGGCCTCAACTCAGACCACATATGGGG
Downstream sequence
GATAAAGGAAAGTCGAGGCCATAAGAAGTTGGGAGGGGCTGAGGTTCTGTACCAGGACAGCAGAAAGGCAGGAGGGCTGCATGCCTGCTTCTTTGAGTGG
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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