Basic Information
VIS ID
TVIS30009939
Fusion event
HIV-PPP1R3F integration
Validated
No
Detection method
QiaQuick PCR and Sequencing
Data source
download(RID)
Sample type
Cell line
Disease
HIV-infected disease (HID)
Quality evaluation
Normal
Reported year
2013
PubMed ID
23953889
Virus Sequence
Virus name
HIV
Reference genome
Not given
Host Sequence
Chromosome
chrX
Cytoband
p11.23
Reference genome
GRCh37/hg19
Start
49132364/49275901 (Hg38)
End
49132364/49275901 (Hg38)
Orient
-
Location type
Intronic
Target gene
PPP1R3F
miRNAs that regulate target gene
hsa-mir-6826-3p ; hsa-mir-4436b-5p ; hsa-mir-6509-3p ; hsa-mir-520f-5p ; hsa-mir-6795-3p ; hsa-mir-6777-3p ; hsa-mir-6887-3p ; hsa-mir-548t-5p ; hsa-mir-548az-5p ; hsa-mir-548n
Nearest miRNA
hsa-mir-1587/Upstream/1688396; hsa-let-7f-2/Downstream/727247;
Nearest TSS
ENST00000429181/Upstream/2847; ENST00000376188/Downstream/4875;
Nearest CpG islands
None/Target, chrX-CpG: 62/Upstream/5164, chrX-CpG: 42/Downstream/46050
Upstream sequence
tactgaattgtaagcttcctagttgggtttgctcaccatggtgtctccaggatccgtcactggggctgatgcacaggaaggcccaCTGTCTTTCAGTGCA
Downstream sequence
CCTATAACTGAAGGGATGGGGATCCAACCTGCTATCTGAGTTGGCAGCCTCAGGGGAAACCAGAATAACTGGAGTTGAACGGGACAAGTCAGGGGCATCT
Reference
Sherrill-Mix, S., et al. HIV latency and integration site placement in five cell-based models.2013, Retrovirology 10: 90.
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