Basic Information
VIS ID
TVIS30000407
Fusion event
HIV-SCP2 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
2016
PubMed ID
26912621
Virus Sequence
Virus name
HIV
Reference genome
K03455.1
Host Sequence
Chromosome
chr1
Cytoband
p32.3
Reference genome
GRCh37/hg19
Start
53419275/52953603 (Hg38)
End
53419275/52953603 (Hg38)
Orient
+
Location type
Intronic
Fragile sites / regions
FRA1B
Target gene
SCP2
miRNAs that regulate target gene
hsa-mir-769-5p ; hsa-mir-26b-5p ; hsa-mir-1260b ; hsa-mir-30a-3p ; hsa-mir-192-3p ; hsa-mir-30d-3p ; hsa-mir-30e-3p ; hsa-mir-511-3p ; hsa-mir-4703-3p ; hsa-mir-4776-3p ; hsa-mir-662 ; hsa-mir-622 ; hsa-mir-4762-5p ; hsa-mir-4733-5p
Nearest miRNA
hsa-mir-12136/Upstream/1117201; hsa-mir-101-1/Downstream/1100476;
Nearest TSS
ENST00000473358/Upstream/11800; ENST00000473584/Downstream/10038;
Nearest CpG islands
None/Target, chr1-CpG: 111/Upstream/25630, chr1-CpG: 106/Downstream/108389
Upstream sequence
cccaactaatttttgtatattttgtagagatggggtcttgccatgttgcccagactggtcttgaactcctggtctcaagcgatacatctgctttggcctc
Downstream sequence
ccaaagctttgagattacaggtgtgattcaccgcacctggccCGATTTTTCCTCTTATCTAGAAGAATATAAAGATTTTCTCTATAATTTTTCTGTTATT
Reference
Sunshine, S., et al. HIV Integration Site Analysis of Cellular Models of HIV Latency with a Probe-Enriched Next-Generation Sequencing Assay. J Virol,2016, 90(9): 4511-4519.
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