Expression analysis of TCGA samples
Basic Information
VIS ID
TVIS10006822
Fusion event
HBV-RBM47 integration
Validated
Yes
Detection method
Alu PCR and sequencing
Data source
Curated
Sample type
Disease
Hepatocellular carcinoma (HCC)
Quality evaluation
Good
Reported year
2015
PubMed ID
Virus Sequence
Virus name
HBV
Reference genome
Not given
Start
1821
Host Sequence
Chromosome
chr4
Cytoband
p14
Reference genome
Start
End
40572142 (Hg38)
Orient
-
Location type
5'UTR
Target gene
miRNAs that regulate target gene
hsa-mir-1-3p ; hsa-mir-124-3p ; hsa-mir-335-5p ; hsa-mir-3658 ; hsa-mir-516b-5p ; hsa-mir-3191-5p ; hsa-mir-3653-3p ; hsa-mir-504-3p ; hsa-mir-298 ; hsa-mir-4670-3p ; hsa-mir-6824-3p ; hsa-mir-6764-3p ; hsa-mir-330-5p ; hsa-mir-326 ; hsa-mir-518c-5p ; hsa-mir-216b-5p ; hsa-mir-122-5p ; hsa-mir-627-3p ; hsa-mir-153-5p ; hsa-mir-1250-3p ; hsa-mir-382-3p ; hsa-mir-129-5p ; hsa-mir-3680-3p ; hsa-mir-557 ; hsa-mir-507 ; hsa-mir-450b-5p ; hsa-mir-4659b-3p ; hsa-mir-4659a-3p ; hsa-mir-6875-3p ; hsa-mir-6881-3p ; hsa-mir-6780a-3p ; hsa-mir-7111-3p ; hsa-mir-4778-3p ; hsa-mir-877-3p
Nearest miRNA
hsa-mir-12113/Upstream/69957; hsa-mir-1243/Downstream/7080527;
Nearest CpG islands
None/Target, chr4-CpG: 46/Upstream/133188, chr4-CpG: 66/Downstream/57581
Upstream sequence
tgtaccactgtactccagcctgggcaacagagcgagactccatctcaaaaagaaaaaaaaaaagaatttatccatgcaactaaacaccacctgttcctca
Downstream sequence
gaggccgaggcgggtggataacctgaggtcaggggttcgaaaccagccttgaccaacctggtgaaaccccctctctactaaaatacaaaaattagctgga
Target sequence
aaaactactggaaaaaaaaaaAAAAACCCACCAGGTgtggctcaccctgtaatcccagcactttgg
Reference
Zhang, X., et al. DNA methylation consistency implicates the primary tumor cell origin of recurrent hepatocellular carcinoma. Epigenomics,2015, 7(4): 581-592.