Basic Information
VIS ID
TVIS30012080
Fusion event
HIV-PDXDC1 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
chr16
Cytoband
p13.11
Reference genome
GRCh37/hg19
Start
15100069/15006212 (Hg38)
End
15100069/15006212 (Hg38)
Orient
+
Location type
Intronic
Fragile sites / regions
FRA16A
Target gene
PDXDC1
miRNAs that regulate target gene
hsa-mir-193b-3p ; hsa-mir-615-3p ; hsa-mir-222-3p
Nearest miRNA
hsa-mir-1225/Upstream/75333; hsa-mir-11401/Downstream/4109;
Nearest TSS
ENST00000527434/Upstream/8464; ENST00000561930/Downstream/3099;
Nearest CpG islands
None/Target, chr16-CpG: 29/Upstream/15905, chr16-CpG: 80/Downstream/49135
Upstream sequence
GGCTTTTTATATCTGAGAATTCCTGGTCTCTACTTGTTTTCATAGTTTCTGCTCTTTATGGAATTGGGTATGGATGGAGGGTTATTGTCTCGCTGCTTGG
Downstream sequence
TAACCTCAGCTGTAATGAGGTGTCAGCCATCTATGATGAGGATGTTTCACATTCCTGTCCTCTCTGCCTGATAAAAGTGACAATTCCTAGCTTGAGAAAA
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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