CNTN4 _LIHC.png
Expression analysis of TCGA samples
Basic Information
VIS ID
TVIS10000515
Fusion event
HBV-CNTN4 integration
Validated
Yes
Detection method
PCR and Sanger sequencing
Data source
Curated
Sample type
Tumor
Disease
Hepatocellular carcinoma (HCC)
Quality evaluation
Perfect
Reported year
2016
PubMed ID
27703150
Virus Sequence
Virus name
HBV
Reference genome
AF090842.1;AB033554.1;AB014381.1;M32138.1;AB032431.1;AB036910.1;AB064310;AY090454.1
Host Sequence
Chromosome
chr3
Cytoband
p26.2
Reference genome
GRCh37/hg19
Start
2895675/2853991 (Hg38)
End
2895675/2853991 (Hg38)
Location type
Intronic
Target gene
CNTN4
miRNAs that regulate target gene
hsa-mir-6736-5p ; hsa-mir-4701-3p ; hsa-mir-1262 ; hsa-mir-6864-3p ; hsa-mir-3672 ; hsa-mir-4504 ; hsa-mir-661 ; hsa-mir-873-3p ; hsa-mir-6776-5p ; hsa-mir-6742-3p ; hsa-mir-6827-3p ; hsa-mir-340-3p ; hsa-mir-5586-3p
Nearest miRNA
hsa-let-7g/Downstream/2396186;
Nearest TSS
ENST00000440867/Upstream/118118; ENST00000473173/Downstream/12429;
Nearest CpG islands
None/Target, chr3-CpG: 148/Upstream/753891, chr3-CpG: 95/Downstream/272649
Downstream sequence
CTTTATTACCAGGTTTGCCAGAAAGGCACTTTTCATCTTCTTAGCAATGCTTCGTCAATTGGTTTTTGGGGAACGGCAGTCATC
Junction sequence
CCGTCCGAAGGTTTTGTACAGCAACAAGAGGGAAACATAGAGGTTACTTGAGCAGGAATCGTGCATTTGTTCAGTGATTTATTACTTTATTACCAGGTTTGCCAGAAAGGCACTTTTCATCTTCTTAGCAATGCTTCGTCAATTGGTTTTTGGGGAACGGCAGTCATC
* Color:  Human Sequence / Virus Sequence / Overlapped sequence / Unknown sequence
Reference
Zhao, L. H., et al.Genomic and oncogenic preference of HBV integration in hepatocellular carcinoma. Nat Commun ,2016,7: 12992.
Curate