Basic Information
VIS ID
TVIS44029240
Fusion event
HTLV-1-SHANK2 integration
Validated
No
Detection method
HTS
Data source
Curated
Sample type
Nontumor
Disease
Not given
Quality evaluation
Normal
Reported year
2019
PubMed ID
30307560
Virus Sequence
Virus name
HTLV-1
Subtype
HTLV-1c
Reference genome
KF242506
Host Sequence
Chromosome
chr11
Cytoband
q13.4
Reference genome
NCBI36/hg18
Start
70103103/70579350 (Hg38)
End
70103103/70579350 (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/295280; hsa-let-7a-2/Downstream/292920;
Nearest TSS
ENST00000527297/Upstream/76491; ENST00000429561/Downstream/51744;
Nearest CpG islands
None/Target, chr11-CpG: 30/Upstream/92042, chr11-CpG: 30/Downstream/82873
Upstream sequence
CCAGCCAGTGAGCTCACTGGGCTACCTTAGCAACTACATGAAACACAGATCAAAGTCCCTCATAGGAGCATGAAGTGTCCCTGAAAAGGCCCAGCTGTGG
Downstream sequence
GACAGGACAATGGTGGCTGCCTCTGAGGACAGCCAGAAGAGGCTGCAGCTGGCACTACATCCCTTCCCTTCCTTCTGCCCAGAAAGTGGCGCTTGCAGGC
Reference
Turpin, J., et al. Impact of Hepatitis B Virus Coinfection on Human T-Lymphotropic Virus Type 1 Clonality in an Indigenous Population of Central Australia. J Infect Dis ,2019,219(4): 562-567.
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