Expression analysis of TCGA samples
Basic Information
VIS ID
TVIS10019667
Fusion event
HBV-chr13 integration
Validated
No
Detection method
VirusFinder
Data source
Curated
Sample type
Disease
Hepatocellular carcinoma (HCC)
Quality evaluation
Normal
Reported year
2017
PubMed ID
Virus Sequence
Virus name
HBV
Reference genome
Start
1784
Integrated sequence
TCAACGACCGACCTTGAGGCATACTTCAAAGACTGTTTGTTTAAAGACTGGGAGGAGTTGGGGGAGGAGATTAGGTTAAAGGTCTTTGTACTAGGAGGCT| |GTAGGCATAAATTGGTCTGCGCACCAGCACCATGCAACTTTTTCACCTCTGCCTAATCATCTCTTGTTCATGTCCTACTGTTCAAGCCTCCAAGCTGTGC
Host Sequence
Chromosome
chr13
Cytoband
q14.11
Reference genome
Start
End
41381401/40807265 (Hg38)
Location type
Intron
miRNAs that regulate target gene
hsa-mir-193b-3p ; hsa-mir-375 ; hsa-mir-7-5p ; hsa-mir-24-3p ; hsa-mir-423-3p ; hsa-mir-218-5p ; hsa-mir-6807-5p ; hsa-mir-5089-5p ; hsa-mir-5589-5p ; hsa-mir-4731-5p ; hsa-mir-6720-3p ; hsa-mir-668-5p ; hsa-mir-4252 ; hsa-mir-6506-5p ; hsa-mir-619-5p ; hsa-mir-3922-3p ; hsa-mir-3176 ; hsa-mir-1273g-3p ; hsa-mir-1295b-3p ; hsa-mir-3186-5p ; hsa-mir-1227-3p ; hsa-mir-1976 ; hsa-mir-3653-5p ; hsa-mir-4279 ; hsa-mir-4537 ; hsa-mir-455-3p ; hsa-mir-4722-3p ; hsa-mir-6499-3p ; hsa-mir-6516-5p ; hsa-mir-6727-3p ; hsa-mir-6747-3p
Nearest miRNA
hsa-mir-2276/Upstream/79378; hsa-mir-1267/Downstream/3501;
Nearest CpG islands
None/Target, chr13-CpG: 551/Upstream/17082, chr13-CpG: 43/Downstream/114375
Upstream sequence
aataaaaataaaatttaaaattacttaaaaataataaattGGCTTACAAATACAAATTAGCATTATTAAGACAACAATATTAAGAATTATATTTTACTGA
Downstream sequence
AGTTTTTTTctgtgataagagttatttcatacatgagtttattttgtcttcataaatacctatttgatatatgagaaaactgagtcttagaaaggttaag
Reference
Cancer Genome Atlas Research Network. Electronic address, w. b. e. and N. Cancer Genome Atlas Research . Comprehensive and Integrative Genomic Characterization of Hepatocellular Carcinoma. Cell ,2017,169(7): 1327-1341 e13