Basic Information
VIS ID
TVIS30005087
Fusion event
HIV-VPS13D 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
p36.22
Reference genome
GRCh37/hg19
Start
12407290/12347233 (Hg38)
End
12407290/12347233 (Hg38)
Orient
-
Location type
Intronic
Fragile sites / regions
FRA1A
Target gene
VPS13D
miRNAs that regulate target gene
hsa-mir-132-3p ; hsa-mir-128-3p ; hsa-mir-7-5p ; hsa-mir-342-5p ; hsa-mir-10a-3p ; hsa-let-7e-5p ; hsa-mir-8485 ; hsa-mir-6868-3p ; hsa-mir-6881-3p ; hsa-mir-6780a-3p ; hsa-mir-7111-3p ; hsa-mir-9-3p ; hsa-mir-7106-3p ; hsa-mir-20a-3p ; hsa-mir-6728-3p ; hsa-mir-6817-3p ; hsa-mir-4685-3p ; hsa-mir-4287 ; hsa-mir-3667-3p ; hsa-mir-6769b-3p ; hsa-mir-6734-3p ; hsa-mir-4723-3p ; hsa-mir-3183 ; hsa-mir-5088-3p ; hsa-mir-4429 ; hsa-mir-320d ; hsa-mir-320c ; hsa-mir-320b ; hsa-mir-320a
Nearest miRNA
hsa-mir-12136/Upstream/155460; hsa-mir-101-1/Downstream/231724;
Nearest TSS
ENST00000473358/Upstream/2368; ENST00000466732/Downstream/9118;
Nearest CpG islands
None/Target, chr1-CpG: 111/Upstream/116091, chr1-CpG: 18/Downstream/193088
Upstream sequence
TAGGCCTGAACAATATCAAGGTTTGAAACAACATCAGGAtttcttttttttttttgagacggagtctcgctctgttgcccaggctggaatgcagtggtgc
Downstream sequence
cgtctcagctcactgcaacatccgccccccgggttcaagcaattctcttgcctcagcctcccaagtagctgggactacaggcacctgccaccacccccgg
Reference
Sherrill-Mix, S., et al. HIV latency and integration site placement in five cell-based models.2013, Retrovirology 10: 90.
Curate