Basic Information
VIS ID
TVIS44033019
Fusion event
HTLV-1-SMARCC1 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
chr3
Cytoband
p21.31
Reference genome
NCBI36/hg18
Start
47647901/47631407 (Hg38)
End
47647901/47631407 (Hg38)
Orient
-
Location type
Intronic
Target gene
SMARCC1
miRNAs that regulate target gene
hsa-mir-1-3p ; hsa-mir-34a-5p ; hsa-mir-98-5p ; hsa-let-7b-5p ; hsa-mir-29b-3p ; hsa-let-7f-5p ; hsa-let-7c-5p ; hsa-mir-320c ; hsa-mir-544a ; hsa-mir-6738-3p ; hsa-mir-570-3p ; hsa-mir-4793-3p ; hsa-mir-3130-3p ; hsa-mir-3140-5p ; hsa-mir-4705 ; hsa-mir-34b-3p
Nearest miRNA
hsa-mir-12127/Upstream/2769426; hsa-let-7g/Downstream/218148;
Nearest TSS
ENST00000440867/Upstream/20609; ENST00000472718/Downstream/46958;
Nearest CpG islands
None/Target, chr3-CpG: 148/Upstream/51766, chr3-CpG: 109/Downstream/150024
Nearest cancer related gene
SMARCC1(TSG, No orient, 0)
Upstream sequence
ACGTATATATGAGGTGGTTTGTAGAATAAATTCAAAGGAAATATCTGTGGTTTTAAGAAAATGTGATCTCTGCTTTCTTGGAAGAACTGAACCTACTACT
Downstream sequence
GCTGACAAAAAGAGAACATGCTCTAATATGGGGGATTTATAGTTTATCCTGGCAATAGTTCTGGGCCTTCCTTCTCCTCTAAGCCTAAAGACCCAGATAG
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.
Curate