SLC35F3 _LIHC.png
Expression analysis of TCGA samples
Basic Information
VIS ID
TVIS10014808
Fusion event
HBV-SLC35F3 integration
Validated
No
Detection method
WGS
Data source
Curated
Sample type
Tumor
Disease
Hepatocellular carcinoma (HCC)
Quality evaluation
Normal
Reported year
2016
PubMed ID
27064257
Virus Sequence
Virus name
HBV
Reference genome
AB033550.1
Start
1757
Orient
+
Integrated sequence
GAGGACTCTTGGACTCTCATCAATGTCAACGACCGACCTTGAGGCATACTTCAAAGACTGTTTGTTTAAGGACTGGGAGGAGTTGGGGGAGGAGATTAGG| |TTAAAGGTCTTTGTACTAGGAGGCTGTAGGCATAAATTGGTCTGTTCACCAGCACCATGCAACTTTTTCACCTCTGCCTAATCATCTCATGTTCATGTCC
Host Sequence
Chromosome
chr1
Cytoband
q42.2
Reference genome
GRCh37/hg19
Start
234101885/233966139 (Hg38)
End
234101885/233966139 (Hg38)
Orient
+
Location type
Intronic
Fragile sites / regions
FRA1H
Target gene
SLC35F3
miRNAs that regulate target gene
hsa-mir-124-3p ; hsa-mir-215-5p ; hsa-mir-192-5p
Nearest miRNA
hsa-mir-101-1/Upstream/341920; hsa-mir-1537/Downstream/340328;
Nearest TSS
ENST00000473358/Upstream/61206; ENST00000366617/Downstream/248132;
Nearest CpG islands
None/Target, chr1-CpG: 111/Upstream/60428, chr1-CpG: 63/Downstream/247999
Upstream sequence
GATAGAGAGTGGCCAAGACCAGCCCTTAGGCCAAACCCCAGCCTGCCTCCACCCACAAGAGGGAAATGGTCTTCCAGTAAGTTATTTATAGGCAACAGAG
Downstream sequence
GTTGTTAGCAGCCAGCAGAAAAAGCTTACATTTGGGAAGAAAAAGTACCAAGATAGCAAAAGTGAAGAAAAGACTAGTGGTAAAGAAAAAAGAGATAAGA
Reference
Fujimoto, A., et al. Whole-genome mutational landscape and characterization of noncoding and structural mutations in liver cancer. Nat Genet ,2016,48(5): 500-509.
Curate