Basic Information
VIS ID
TVIS44009339
Fusion event
HTLV-1-MSH2 integration
Validated
No
Detection method
HTS
Data source
download(RID)
Sample type
Nontumor
Disease
Adult T-cell leukemia (ATL)
Quality evaluation
Normal
Reported year
2014
PubMed ID
24735963
Virus Sequence
Virus name
HTLV-1
Reference genome
Not given
Host Sequence
Chromosome
chr2
Cytoband
p16.3
Reference genome
GRCh37/hg19
Start
47747185/47520046 (Hg38)
End
47747185/47520046 (Hg38)
Orient
-
Location type
Intronic
Fragile sites / regions
FRA2S
Target gene
MSH2
miRNAs that regulate target gene
hsa-mir-155-5p ; hsa-mir-16-5p ; hsa-mir-15a-5p ; hsa-mir-21-5p ; hsa-mir-1-3p ; hsa-mir-101-3p ; hsa-mir-183-5p ; hsa-mir-3163
Nearest miRNA
hsa-mir-1301/Upstream/142276; hsa-mir-10b/Downstream/1539557;
Nearest TSS
ENST00000437798/Upstream/43537; ENST00000435331/Downstream/7491;
Nearest CpG islands
None/Target, chr2-CpG: 135/Upstream/116394, chr2-CpG: 103/Downstream/806
Nearby gene
KCNK12(-730) ;
Nearest cancer related gene
MSH2(TSG, No orient, 0)
Upstream sequence
TCTTAAAGGGGGAAAAGTTGAACTGATCAACAGTAGTTAAGAAAAAAAAAATCCACACCAACAAATAAATATCTTGTCTGAGAAGACTCAGATATTCCTG
Downstream sequence
GTTAATATTGAAAAGCACTGCTGTGGATGAGCTTGTGAAAGAAAGGACGGTTGGGGGATTCAAGATCTGCCGATCCGAGCCTGGAGATCAGCCAGCTAAA
Reference
Cook, L. B., et al. The role of HTLV-1 clonality, proviral structure, and genomic integration site in adult T-cell leukemia/lymphoma. Blood,2014, 123(25): 3925-3931.
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