Basic Information
VIS ID
TVIS30007956
Fusion event
HIV-SLX4IP 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
chr20
Cytoband
p12.2
Reference genome
GRCh37/hg19
Start
10519167/10538519 (Hg38)
End
10519167/10538519 (Hg38)
Orient
-
Location type
Intronic
Fragile sites / regions
FRA20B
Target gene
SLX4IP
miRNAs that regulate target gene
hsa-mir-335-5p ; hsa-mir-665 ; hsa-mir-7977 ; hsa-mir-6884-5p ; hsa-mir-485-5p ; hsa-mir-4524a-3p ; hsa-mir-20b-3p ; hsa-mir-3137 ; hsa-mir-4329 ; hsa-mir-3664-3p ; hsa-mir-4433a-3p ; hsa-mir-4459 ; hsa-mir-4768-3p ; hsa-mir-5690 ; hsa-mir-4757-3p ; hsa-mir-2114-5p ; hsa-mir-5588-3p ; hsa-mir-4478 ; hsa-mir-4419b ; hsa-mir-3929 ; hsa-mir-4695-5p ; hsa-mir-4524b-3p ; hsa-mir-510-5p ; hsa-mir-512-5p
Nearest miRNA
hsa-mir-103a-2/Upstream/3166827; hsa-mir-1-1/Downstream/111117;
Nearest TSS
ENST00000382410/Upstream/103216; ENST00000488816/Downstream/60156;
Nearest CpG islands
None/Target, chr20-CpG: 39/Upstream/104174, chr20-CpG: 255/Downstream/133406
Upstream sequence
agtcctaaatgtttccagacattgtacacagggaggaagggagcaaaatcacctcttgattaagaatcTAAAATTACAGTTCTAGATTCTTATTGATAAA
Downstream sequence
GCCCTTCATCttttttttttttttgagacagagtctcactctgtcgcccaggctggagtgcagtggtgccatcttggctcactgcaacctctgcctcctg
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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