Basic Information
VIS ID
TVIS44012909
Fusion event
HTLV-1-SGMS1 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
chr10
Cytoband
q11.23
Reference genome
GRCh37/hg19
Start
52280461/50520701 (Hg38)
End
52280461/50520701 (Hg38)
Orient
-
Location type
Intronic
Fragile sites / regions
FRA10G
Target gene
SGMS1
miRNAs that regulate target gene
hsa-mir-130b-3p ; hsa-mir-124-3p ; hsa-mir-98-5p ; hsa-mir-93-5p ; hsa-mir-33a-5p ; hsa-mir-744-5p ; hsa-mir-142-3p ; hsa-mir-4477a ; hsa-mir-4775 ; hsa-mir-5094 ; hsa-mir-4328 ; hsa-mir-32-3p ; hsa-mir-519c-3p ; hsa-mir-519b-3p ; hsa-mir-519a-3p ; hsa-mir-526b-3p ; hsa-mir-519d-3p ; hsa-mir-20b-5p ; hsa-mir-20a-5p ; hsa-mir-17-5p ; hsa-mir-106b-5p ; hsa-mir-106a-5p ; hsa-mir-548t-5p ; hsa-mir-548az-5p ; hsa-mir-27b-3p ; hsa-mir-27a-3p ; hsa-mir-181c-5p ; hsa-let-7a-3p ; hsa-let-7b-3p ; hsa-let-7f-1-3p ; hsa-mir-125b-1-3p ; hsa-mir-1273g-5p ; hsa-mir-186-3p ; hsa-mir-300 ; hsa-mir-323a-5p ; hsa-mir-3621 ; hsa-mir-3656 ; hsa-mir-379-3p ; hsa-mir-380-3p ; hsa-mir-381-3p ; hsa-mir-3924 ; hsa-mir-411-3p ; hsa-mir-4495 ; hsa-mir-4666a-3p ; hsa-mir-4733-5p ; hsa-mir-520d-5p ; hsa-mir-524-5p ; hsa-mir-605-5p ; hsa-mir-656-5p ; hsa-mir-876-3p ; hsa-mir-98-3p
Nearest miRNA
hsa-mir-1265/Upstream/1535114; hsa-mir-107/Downstream/778872;
Nearest TSS
ENST00000439456/Upstream/47887; ENST00000609579/Downstream/103276;
Nearest CpG islands
None/Target, chr10-CpG: 68/Upstream/102279, chr10-CpG: 256/Downstream/102011
Nearest cancer related gene
SGMS1(TSG, No orient, 0)
Upstream sequence
agctctaccaacccttgctccaaactcttccatgacaccataTAACAAAATAGTTTCAACTTGAACAGCAATATTTATTCTTTCTTCCTGCATAGATACT
Downstream sequence
CATAGATACGCCAACAGAGATAGAATGGCTTTGCATGCTAAGTGACTGACACTGCGATAGGATTAATGTATTTAGCACAGACAACCCAAAGGGTAGAAAA
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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