Basic Information
VIS ID
TVIS30011477
Fusion event
HIV-SMC3 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
chr10
Cytoband
q25.2
Reference genome
GRCh37/hg19
Start
112342794/110583036 (Hg38)
End
112342794/110583036 (Hg38)
Orient
+
Location type
Intronic
Fragile sites / regions
FRA10D ; FRA10A ; FRA10B
Target gene
SMC3
miRNAs that regulate target gene
hsa-mir-340-5p ; hsa-mir-196a-5p ; hsa-mir-615-3p ; hsa-mir-193b-3p ; hsa-mir-92a-3p ; hsa-mir-3163 ; hsa-let-7a-2-3p ; hsa-let-7g-3p ; hsa-mir-382-5p ; hsa-mir-3613-5p ; hsa-mir-526b-5p ; hsa-mir-27b-5p ; hsa-mir-4680-3p ; hsa-mir-5187-3p ; hsa-mir-4427 ; hsa-mir-4762-5p ; hsa-mir-4668-3p ; hsa-mir-493-5p ; hsa-let-7c-3p ; hsa-mir-524-5p ; hsa-mir-520d-5p ; hsa-mir-302a-5p ; hsa-mir-4700-3p ; hsa-mir-10a-3p ; hsa-mir-7844-5p
Nearest miRNA
hsa-mir-107/Upstream/6314631; hsa-mir-202/Downstream/315054;
Nearest TSS
ENST00000439456/Upstream/14709; ENST00000471172/Downstream/61361;
Nearest CpG islands
None/Target, chr10-CpG: 68/Upstream/14606, chr10-CpG: 137/Downstream/60159
Upstream sequence
tttttttttttggaagacagggtctcactccattgcacaggctggagtgcagtggtgagatcacagctcactgcagccttgatctctcaagctcaagtga
Downstream sequence
tcctcccacctcagcctcctatttttgttattttttgaagagatggaatctcagtatgttgcccaggctggttttgaactcctgggttcaaggagtcctc
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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