Basic Information
VIS ID
TVIS30010076
Fusion event
HIV-NDC1 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
p32.3
Reference genome
GRCh37/hg19
Start
54243625/53777952 (Hg38)
End
54243625/53777952 (Hg38)
Orient
+
Location type
Intronic
Fragile sites / regions
FRA1B
Target gene
NDC1
miRNAs that regulate target gene
hsa-mir-421 ; hsa-mir-7-5p ; hsa-mir-125b-5p ; hsa-mir-222-3p ; hsa-mir-181b-5p
Nearest miRNA
hsa-mir-12136/Upstream/1941550; hsa-mir-101-1/Downstream/276127;
Nearest TSS
ENST00000473358/Upstream/39846; ENST00000526329/Downstream/60511;
Nearest CpG islands
None/Target, chr1-CpG: 111/Upstream/38315, chr1-CpG: 54/Downstream/60133
Upstream sequence
ataggcgtgtgcacctccccacctaaattttgttgttgctgttgttggagacgggatttcaccatgttgaccaggggctcaagcaatccatcagtcttgg
Downstream sequence
ccttccaaagtgctgggattacatgtgtgtgccaccgcgcccggAGAATCTTTTTTTTTTTAAAGTGATGTGATGTTGTAACAAAAGATGTAAATCTTTT
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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