SCML4 _LIHC.png
Expression analysis of TCGA samples
Basic Information
VIS ID
TVIS10015621
Fusion event
HBV-SCML4 integration
Validated
No
Detection method
MAPS
Data source
Curated
Sample type
Adjacent tissue
Disease
Hepatocellular carcinoma (HCC)
Quality evaluation
Perfect
Reported year
2012
PubMed ID
23236287
Virus Sequence
Virus name
HBV
Reference genome
AY800389.1;AY800390.1;AY800391.1;AY800392.1
Orient
+
Host Sequence
Chromosome
chr6
Cytoband
q21
Reference genome
GRCh37/hg19
Start
108041230/107720026 (Hg38)
End
108041230/107720026 (Hg38)
Orient
+
Location type
Intronic
Fragile sites / regions
FRA6F
Target gene
SCML4
miRNAs that regulate target gene
hsa-mir-510-3p ; hsa-mir-2052 ; hsa-mir-8065 ; hsa-mir-570-3p ; hsa-mir-6876-5p ; hsa-mir-4476 ; hsa-mir-5582-3p
Nearest miRNA
hsa-mir-10398/Upstream/935806; hsa-mir-1202/Downstream/11349021;
Nearest TSS
ENST00000381078/Upstream/85036; ENST00000606070/Downstream/12077;
Nearest CpG islands
None/Target, chr6-CpG: 120/Upstream/84537, chr6-CpG: 32/Downstream/128166
Upstream sequence
AAAATTCCCCCAATGCTGGTTGTAATGCCA
Junction sequence
AAAATTCCCCCAATGCTGGTTGTAATGCCACTCCCCCAACTCCTCCCAGTCCTTAAACAACCAGTCTTTGCAGTATGCCTCAAGGTCG
* Color:  Human Sequence / Virus Sequence / Overlapped sequence / Unknown sequence
Reference
Ding, D., et al. Recurrent targeted genes of hepatitis B virus in the liver cancer genomes identified by a next-generation sequencing-based approach. PLoS Genet ,2010,8(12): e1003065.
Curate