Basic Information
VIS ID
TVIS30002393
Fusion event
HIV-RAB40C 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
p13.3
Reference genome
GRCh37/hg19
Start
666375/616375 (Hg38)
End
666375/616375 (Hg38)
Orient
+
Location type
Intronic
Target gene
RAB40C
miRNAs that regulate target gene
hsa-mir-484 ; hsa-let-7a-5p ; hsa-mir-1224-5p ; hsa-mir-4792 ; hsa-mir-4451 ; hsa-mir-7854-3p ; hsa-mir-4751 ; hsa-mir-5004-5p ; hsa-mir-3663-3p ; hsa-mir-1825 ; hsa-mir-4459 ; hsa-mir-512-3p ; hsa-mir-6831-5p ; hsa-mir-3927-3p ; hsa-let-7c-5p ; hsa-let-7d-5p ; hsa-let-7e-5p ; hsa-let-7f-5p ; hsa-let-7g-5p ; hsa-mir-4458 ; hsa-mir-4500 ; hsa-mir-98-5p ; hsa-let-7b-5p ; hsa-let-7i-5p ; hsa-mir-29c-3p ; hsa-mir-29b-3p ; hsa-mir-29a-3p ; hsa-mir-4730 ; hsa-mir-4644 ; hsa-mir-25-5p ; hsa-mir-4306 ; hsa-mir-185-5p ; hsa-mir-589-5p ; hsa-mir-5739 ; hsa-mir-5091 ; hsa-mir-3925-5p
Nearest miRNA
hsa-mir-3176/Upstream/73009; hsa-mir-11401/Downstream/153808;
Nearest TSS
ENST00000527434/Upstream/26043; ENST00000564703/Downstream/270;
Nearest CpG islands
None/Target, chr16-CpG: 29/Upstream/1788, chr16-CpG: 29/Downstream/4250
Upstream sequence
ATGTGGCAGGCAGGCTGGTGGCTGTCTGAGGTCAGTCCAGAGTCCGGAGAAGCAGCATtttatttatttatttatttatttatttatttattGAGTActg
Downstream sequence
tcacccaggcaggagtgcagtgacatgatctcggctcactgcaacctccacctcccagcttcaagtgattctcctgcctcagcctcccgagtagctggga
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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