Basic Information
VIS ID
TVIS44009071
Fusion event
HTLV-1-GCM1 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
chr6
Cytoband
p12.1
Reference genome
GRCh37/hg19
Start
53054495/53189697 (Hg38)
End
53054495/53189697 (Hg38)
Orient
-
Location type
Intronic
Target gene
GCM1
miRNAs that regulate target gene
hsa-mir-19b-3p ; hsa-mir-515-5p ; hsa-mir-1247-3p ; hsa-mir-1273f ; hsa-mir-1827 ; hsa-mir-1910-3p ; hsa-mir-2467-3p ; hsa-mir-3612 ; hsa-mir-377-5p ; hsa-mir-4252 ; hsa-mir-4257 ; hsa-mir-4537 ; hsa-mir-455-3p ; hsa-mir-566 ; hsa-mir-6086 ; hsa-mir-6499-3p ; hsa-mir-650 ; hsa-mir-6511a-5p ; hsa-mir-6516-5p ; hsa-mir-652-3p ; hsa-mir-6715a-3p ; hsa-mir-6715b-3p ; hsa-mir-6789-3p ; hsa-mir-371a-5p ; hsa-mir-888-5p
Nearest miRNA
hsa-mir-10398/Upstream/1040656; hsa-mir-10524/Downstream/87296;
Nearest TSS
ENST00000381078/Upstream/40868; ENST00000605281/Downstream/159229;
Nearest CpG islands
None/Target, chr6-CpG: 120/Upstream/123737, chr6-CpG: 127/Downstream/158122
Nearby gene
GCM1(-40871) ;
Upstream sequence
CTTTCTTGAGAGTCATGATTATATTTAGCAACTTAAATCATTGCCACTGAAAAGCTTGGCTTCAGTTTTAAGCAACTAATCTAAAAGCTATGGCACAGAG
Downstream sequence
CTTGCAAGGTGTGGGCTCTAAAGGGTTACATTACATAGCTAAATCATATAGTTGCTTGGCTGCCTTTATGctagacatcaagtcaggcaactggaattca
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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