Basic Information
VIS ID
TVIS30005465
Fusion event
HIV-PTPRC 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
chr1
Cytoband
q31.3
Reference genome
GRCh37/hg19
Start
198640332/198671203 (Hg38)
End
198640332/198671203 (Hg38)
Orient
-
Location type
Intronic
Fragile sites / regions
FRA1K
Target gene
PTPRC
miRNAs that regulate target gene
hsa-mir-1238-3p ; hsa-mir-670-3p ; hsa-mir-4309 ; hsa-mir-3198 ; hsa-mir-4653-3p ; hsa-mir-4748 ; hsa-mir-4464
Nearest miRNA
hsa-mir-101-1/Upstream/2088722; hsa-mir-1182/Downstream/187670;
Nearest TSS
ENST00000473358/Upstream/4142; ENST00000484135/Downstream/25678;
Nearest CpG islands
None/Target, chr1-CpG: 111/Upstream/511969, chr1-CpG: 36/Downstream/1364143
Nearest cancer related gene
PTPRC(TSG, No orient, 0)
Upstream sequence
AATTTTTTGAAATGTAAAAAAaaaaaatttttctagcctcccagtctacactctcacttttcactaacccatttactgctttcttgcttgttctcccagc
Downstream sequence
acaccacaaaaacaacttccatgcatacaccagtatcacccccctcacccccctgtttccaataaattaaacccaatggaccaagctaaagcatttatta
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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