Basic Information
VIS ID
TVIS44011798
Fusion event
HTLV-1-SHANK2 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
chr11
Cytoband
q13.3
Reference genome
GRCh37/hg19
Start
70340864/70494759 (Hg38)
End
70340864/70494759 (Hg38)
Orient
-
Location type
Intronic
Fragile sites / regions
FRA11H
Target gene
SHANK2
miRNAs that regulate target gene
hsa-mir-1307-3p ; hsa-mir-155-5p ; hsa-mir-4646-3p ; hsa-mir-4433b-5p ; hsa-mir-4433a-5p ; hsa-mir-4469 ; hsa-mir-4667-3p ; hsa-mir-1470 ; hsa-mir-6756-3p ; hsa-mir-3127-3p
Nearest miRNA
hsa-mir-10392/Upstream/210689; hsa-let-7a-2/Downstream/377511;
Nearest TSS
ENST00000527297/Upstream/19589; ENST00000429561/Downstream/8100;
Nearest CpG islands
None/Target, chr11-CpG: 30/Upstream/7451, chr11-CpG: 30/Downstream/167464
Upstream sequence
tggctgtcacgcccagcacacttaccatggggcccttcagggaggtgtttgccgacccctgGCCTGGACCACGTTTCCAGTTGTCAGCAAAATGCCAAGT
Downstream sequence
GTTCACGCAAAGCAAGAAAGCCCTTGCCCCATAGTGTCCGGGCAGCCAAATCTCCCCCCACAGCACTCTCTCCCTTCATGACCAAGTCCAGCTGACCAGG
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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