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VISDB
Viral Integration Site DataBase
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TVIS30015592
Basic Information
VIS ID
TVIS30015592
Fusion event
HIV-SMCHD1 integration
Validated
Yes
Detection method
LM PCR
Data source
Curated
Sample type
PBMC
Disease
HIV-infected disease (HID)
Quality evaluation
Good
Reported year
2014
PubMed ID
24968937
Virus Sequence
Virus name
HIV
Reference genome
Not given
Host Sequence
Chromosome
chr18
Cytoband
p11.32
Reference genome
GRCh37/hg19
Start
2706187/2706189 (Hg38)
End
2706274/2706189 (Hg38)
Orient
+
Location type
Intronic
Target gene
SMCHD1
miRNAs that regulate target gene
hsa-mir-210-3p
;
hsa-mir-132-3p
;
hsa-mir-128-3p
;
hsa-mir-181a-5p
;
hsa-mir-877-5p
;
hsa-mir-421
;
hsa-mir-149-5p
;
hsa-mir-221-3p
;
hsa-mir-10b-5p
;
hsa-mir-10a-5p
;
hsa-mir-100-5p
;
hsa-mir-30a-5p
;
hsa-mir-18a-5p
;
hsa-mir-6768-5p
;
hsa-mir-1277-5p
;
hsa-mir-4789-5p
;
hsa-mir-3941
;
hsa-mir-5011-5p
;
hsa-mir-603
;
hsa-mir-362-3p
;
hsa-mir-329-3p
;
hsa-mir-8485
;
hsa-mir-1264
;
hsa-mir-3184-3p
;
hsa-mir-510-3p
;
hsa-mir-203a-3p
;
hsa-mir-190a-3p
Nearest miRNA
hsa-mir-8078/Upstream/2593850; hsa-mir-1-2/Downstream/1179164;
Nearest TSS
ENST00000575820/Upstream/2495;
ENST00000581711/Downstream/254;
Nearest CpG islands
None/Target,
chr18-CpG: 67/Upstream/49371
,
chr18-CpG: 150/Downstream/140378
Nearest cancer related gene
SMCHD1
(TSG, No orient, 0)
Upstream sequence
ccagaattctatctcagcaatgagtaactacaaaactggagtgggttttttccctataccatgctTTCTTGTTAATGTTTGATATGTTAGGACTACAGAG
Downstream sequence
CTTTGGAAGAAACAAATGGGTGTTTGTTTTTATTACAGCTAGATTTAAATAGTTTTCTTTGAAATGTTGGTAAATGTATTTATTCAGGAACCTCAGGCAC
Target sequence
GTTATATAAAAAATATAAACAAACATTGTGGTGTAACGTAAGAATAGCTACTGTTATTTATGTACTTAATTAGGATAAAATATATTT
Reference
Maldarelli, F., et al. Specific HIV integration sites are linked to clonal expansion and persistence of infected cells. Science,2014, 345(6193): 179-183.
Sample Information
×
Sample name
PT2
Sample type
PBMC
Age
25
Gender
Female
CpG Island Information
×
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